data_3NVF
#
_entry.id 3NVF
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.387
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 3NVF pdb_00003nvf 10.2210/pdb3nvf/pdb
RCSB RCSB060327 ? ?
WWPDB D_1000060327 ? ?
#
loop_
_pdbx_audit_revision_history.ordinal
_pdbx_audit_revision_history.data_content_type
_pdbx_audit_revision_history.major_revision
_pdbx_audit_revision_history.minor_revision
_pdbx_audit_revision_history.revision_date
1 'Structure model' 1 0 2011-03-02
2 'Structure model' 1 1 2011-07-13
3 'Structure model' 1 2 2024-02-21
#
_pdbx_audit_revision_details.ordinal 1
_pdbx_audit_revision_details.revision_ordinal 1
_pdbx_audit_revision_details.data_content_type 'Structure model'
_pdbx_audit_revision_details.provider repository
_pdbx_audit_revision_details.type 'Initial release'
_pdbx_audit_revision_details.description ?
_pdbx_audit_revision_details.details ?
#
loop_
_pdbx_audit_revision_group.ordinal
_pdbx_audit_revision_group.revision_ordinal
_pdbx_audit_revision_group.data_content_type
_pdbx_audit_revision_group.group
1 2 'Structure model' 'Version format compliance'
2 3 'Structure model' 'Data collection'
3 3 'Structure model' 'Database references'
4 3 'Structure model' 'Derived calculations'
#
loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
1 3 'Structure model' chem_comp_atom
2 3 'Structure model' chem_comp_bond
3 3 'Structure model' database_2
4 3 'Structure model' struct_site
#
loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
1 3 'Structure model' '_database_2.pdbx_DOI'
2 3 'Structure model' '_database_2.pdbx_database_accession'
3 3 'Structure model' '_struct_site.pdbx_auth_asym_id'
4 3 'Structure model' '_struct_site.pdbx_auth_comp_id'
5 3 'Structure model' '_struct_site.pdbx_auth_seq_id'
#
_pdbx_database_status.entry_id 3NVF
_pdbx_database_status.status_code REL
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.recvd_initial_deposition_date 2010-07-08
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.SG_entry ?
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.db_id
_pdbx_database_related.details
_pdbx_database_related.content_type
PDB 3NVE 'MMHFGN hexapeptide (residues 138-143) from golden hamster prion protein' unspecified
PDB 3NVG 'MIHFGN hexapeptide (residues 137-142) from mouse prion protein' unspecified
PDB 3NVH 'MIHFGND (residues 137-143) from mouse prion protein' unspecified
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Apostol, M.I.' 1
'Sawaya, M.R.' 2
'Eisenberg, D.' 3
#
_citation.id primary
_citation.title 'Atomic structures suggest determinants of transmission barriers in Mammalian prion disease.'
_citation.journal_abbrev Biochemistry
_citation.journal_volume 50
_citation.page_first 2456
_citation.page_last 2463
_citation.year 2011
_citation.journal_id_ASTM BICHAW
_citation.country US
_citation.journal_id_ISSN 0006-2960
_citation.journal_id_CSD 0033
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 21323366
_citation.pdbx_database_id_DOI 10.1021/bi101803k
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Apostol, M.I.' 1 ?
primary 'Wiltzius, J.J.' 2 ?
primary 'Sawaya, M.R.' 3 ?
primary 'Cascio, D.' 4 ?
primary 'Eisenberg, D.' 5 ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer syn 'Major prion protein' 673.781 1 ? ? ? ?
2 non-polymer syn '(4S)-2-METHYL-2,4-PENTANEDIOL' 118.174 1 ? ? ? ?
#
_entity_name_com.entity_id 1
_entity_name_com.name 'PrP, PrP27-30, PrP33-35C, ASCR'
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code IIHFGS
_entity_poly.pdbx_seq_one_letter_code_can IIHFGS
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
_pdbx_entity_nonpoly.entity_id 2
_pdbx_entity_nonpoly.name '(4S)-2-METHYL-2,4-PENTANEDIOL'
_pdbx_entity_nonpoly.comp_id MPD
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 ILE n
1 2 ILE n
1 3 HIS n
1 4 PHE n
1 5 GLY n
1 6 SER n
#
_pdbx_entity_src_syn.entity_id 1
_pdbx_entity_src_syn.pdbx_src_id 1
_pdbx_entity_src_syn.pdbx_alt_source_flag sample
_pdbx_entity_src_syn.pdbx_beg_seq_num ?
_pdbx_entity_src_syn.pdbx_end_seq_num ?
_pdbx_entity_src_syn.organism_scientific 'Homo sapiens'
_pdbx_entity_src_syn.organism_common_name human
_pdbx_entity_src_syn.ncbi_taxonomy_id 9606
_pdbx_entity_src_syn.details 'IIHFGS (UNP residues 138-143) from human prion'
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067
HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162
ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173
MPD non-polymer . '(4S)-2-METHYL-2,4-PENTANEDIOL' ? 'C6 H14 O2' 118.174
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 ILE 1 1 1 ILE ILE A . n
A 1 2 ILE 2 2 2 ILE ILE A . n
A 1 3 HIS 3 3 3 HIS HIS A . n
A 1 4 PHE 4 4 4 PHE PHE A . n
A 1 5 GLY 5 5 5 GLY GLY A . n
A 1 6 SER 6 6 6 SER SER A . n
#
_pdbx_nonpoly_scheme.asym_id B
_pdbx_nonpoly_scheme.entity_id 2
_pdbx_nonpoly_scheme.mon_id MPD
_pdbx_nonpoly_scheme.ndb_seq_num 1
_pdbx_nonpoly_scheme.pdb_seq_num 7
_pdbx_nonpoly_scheme.auth_seq_num 1
_pdbx_nonpoly_scheme.pdb_mon_id MPD
_pdbx_nonpoly_scheme.auth_mon_id MPD
_pdbx_nonpoly_scheme.pdb_strand_id A
_pdbx_nonpoly_scheme.pdb_ins_code .
#
loop_
_software.pdbx_ordinal
_software.name
_software.version
_software.date
_software.type
_software.contact_author
_software.contact_author_email
_software.classification
_software.location
_software.language
_software.citation_id
1 DENZO . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction'
http://www.hkl-xray.com/ ? ?
2 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling'
http://www.hkl-xray.com/ ? ?
3 PHASER 1.3.2 'Wed Feb 15 11:59:26 2006' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing
http://www-structmed.cimr.cam.ac.uk/phaser/ ? ?
4 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement
http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ?
5 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction'
http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ?
#
_cell.length_a 27.546
_cell.length_b 31.017
_cell.length_c 4.804
_cell.angle_alpha 90.000
_cell.angle_beta 90.000
_cell.angle_gamma 90.000
_cell.entry_id 3NVF
_cell.pdbx_unique_axis ?
_cell.Z_PDB 4
_cell.length_a_esd ?
_cell.length_b_esd ?
_cell.length_c_esd ?
_cell.angle_alpha_esd ?
_cell.angle_beta_esd ?
_cell.angle_gamma_esd ?
#
_symmetry.space_group_name_H-M 'P 21 21 2'
_symmetry.entry_id 3NVF
_symmetry.Int_Tables_number 18
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.space_group_name_Hall ?
#
_exptl.crystals_number 1
_exptl.entry_id 3NVF
_exptl.method 'X-RAY DIFFRACTION'
#
_exptl_crystal.id 1
_exptl_crystal.density_Matthews 1.52
_exptl_crystal.density_meas ?
_exptl_crystal.density_percent_sol 19.23
_exptl_crystal.description ?
_exptl_crystal.F_000 ?
_exptl_crystal.preparation ?
#
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP'
_exptl_crystal_grow.pH 7.4
_exptl_crystal_grow.temp 298
_exptl_crystal_grow.pdbx_details '100mM Tris pH 7.4, 25% MPD, vapor diffusion, hanging drop, temperature 298K'
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pdbx_pH_range ?
#
_diffrn.id 1
_diffrn.ambient_temp 100
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
#
_diffrn_detector.diffrn_id 1
_diffrn_detector.detector CCD
_diffrn_detector.type 'MAR CCD 225'
_diffrn_detector.pdbx_collection_date 2008-01-01
_diffrn_detector.details ?
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.monochromator ?
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 0.8726
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source SYNCHROTRON
_diffrn_source.type 'ESRF BEAMLINE ID13'
_diffrn_source.pdbx_wavelength_list 0.8726
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_synchrotron_site ESRF
_diffrn_source.pdbx_synchrotron_beamline ID13
#
_reflns.entry_id 3NVF
_reflns.d_resolution_high 1.800
_reflns.d_resolution_low 90.000
_reflns.number_obs 443
_reflns.pdbx_Rmerge_I_obs 0.216
_reflns.pdbx_netI_over_sigmaI 6.800
_reflns.pdbx_chi_squared 1.137
_reflns.pdbx_redundancy 3.800
_reflns.percent_possible_obs 85.400
_reflns.observed_criterion_sigma_F ?
_reflns.observed_criterion_sigma_I ?
_reflns.number_all ?
_reflns.pdbx_Rsym_value ?
_reflns.B_iso_Wilson_estimate ?
_reflns.R_free_details ?
_reflns.limit_h_max ?
_reflns.limit_h_min ?
_reflns.limit_k_max ?
_reflns.limit_k_min ?
_reflns.limit_l_max ?
_reflns.limit_l_min ?
_reflns.observed_criterion_F_max ?
_reflns.observed_criterion_F_min ?
_reflns.pdbx_scaling_rejects ?
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
#
loop_
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.number_measured_obs
_reflns_shell.number_measured_all
_reflns_shell.number_unique_obs
_reflns_shell.Rmerge_I_obs
_reflns_shell.meanI_over_sigI_obs
_reflns_shell.pdbx_Rsym_value
_reflns_shell.pdbx_chi_squared
_reflns_shell.pdbx_redundancy
_reflns_shell.percent_possible_obs
_reflns_shell.number_unique_all
_reflns_shell.percent_possible_all
_reflns_shell.pdbx_diffrn_id
_reflns_shell.pdbx_ordinal
1.800 1.940 ? ? ? 0.395 ? ? 1.424 1.700 ? 63 67.000 ? 1
1.940 2.130 ? ? ? 0.327 ? ? 1.294 2.300 ? 83 85.600 ? 2
2.130 2.440 ? ? ? 0.314 ? ? 0.964 3.200 ? 89 78.800 ? 3
2.440 3.080 ? ? ? 0.244 ? ? 1.062 5.400 ? 87 100.000 ? 4
3.080 90.000 ? ? ? 0.197 ? ? 1.199 5.100 ? 121 94.500 ? 5
#
_refine.entry_id 3NVF
_refine.ls_d_res_high 1.8000
_refine.ls_d_res_low 20.6000
_refine.pdbx_ls_sigma_F 0.000
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.ls_percent_reflns_obs 86.4300
_refine.ls_number_reflns_obs 433
_refine.ls_number_reflns_all ?
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.pdbx_R_Free_selection_details RANDOM
_refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS'
_refine.ls_R_factor_all ?
_refine.ls_R_factor_obs 0.2133
_refine.ls_R_factor_R_work 0.2118
_refine.ls_wR_factor_R_work 0.2013
_refine.ls_R_factor_R_free 0.2263
_refine.ls_wR_factor_R_free 0.2521
_refine.ls_percent_reflns_R_free 9.2000
_refine.ls_number_reflns_R_free 40
_refine.ls_R_factor_R_free_error ?
_refine.B_iso_mean 20.8202
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.pdbx_isotropic_thermal_model ?
_refine.aniso_B[1][1] 1.0000
_refine.aniso_B[2][2] -0.0400
_refine.aniso_B[3][3] -0.9500
_refine.aniso_B[1][2] 0.0000
_refine.aniso_B[1][3] 0.0000
_refine.aniso_B[2][3] 0.0000
_refine.correlation_coeff_Fo_to_Fc 0.9550
_refine.correlation_coeff_Fo_to_Fc_free 0.9400
_refine.overall_SU_R_Cruickshank_DPI 0.2379
_refine.overall_SU_R_free 0.1668
_refine.pdbx_overall_ESU_R_Free 0.1670
_refine.overall_SU_ML 0.1110
_refine.overall_SU_B 4.0090
_refine.solvent_model_details MASK
_refine.pdbx_solvent_vdw_probe_radii 1.4000
_refine.pdbx_solvent_ion_probe_radii 0.8000
_refine.pdbx_solvent_shrinkage_radii 0.8000
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.pdbx_starting_model ?
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD'
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.overall_FOM_work_R_set 0.8682
_refine.B_iso_max 52.980
_refine.B_iso_min 10.200
_refine.occupancy_max 1.000
_refine.occupancy_min 1.000
_refine.pdbx_ls_sigma_I ?
_refine.ls_redundancy_reflns_obs ?
_refine.ls_R_factor_R_free_error_details ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.overall_FOM_free_R_set ?
_refine.pdbx_overall_phase_error ?
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.pdbx_overall_ESU_R ?
_refine.pdbx_diffrn_id 1
_refine.pdbx_TLS_residual_ADP_flag ?
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
#
_refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 48
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 8
_refine_hist.number_atoms_solvent 0
_refine_hist.number_atoms_total 56
_refine_hist.d_res_high 1.8000
_refine_hist.d_res_low 20.6000
#
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.pdbx_restraint_function
r_bond_refined_d 56 0.009 0.021 ? 'X-RAY DIFFRACTION' ?
r_bond_other_d 35 0.001 0.020 ? 'X-RAY DIFFRACTION' ?
r_angle_refined_deg 75 1.657 2.043 ? 'X-RAY DIFFRACTION' ?
r_angle_other_deg 84 0.693 3.000 ? 'X-RAY DIFFRACTION' ?
r_dihedral_angle_1_deg 5 9.100 5.000 ? 'X-RAY DIFFRACTION' ?
r_dihedral_angle_2_deg 2 52.201 20.000 ? 'X-RAY DIFFRACTION' ?
r_dihedral_angle_3_deg 7 10.817 15.000 ? 'X-RAY DIFFRACTION' ?
r_chiral_restr 8 0.053 0.200 ? 'X-RAY DIFFRACTION' ?
r_gen_planes_refined 52 0.004 0.020 ? 'X-RAY DIFFRACTION' ?
r_gen_planes_other 12 0.001 0.020 ? 'X-RAY DIFFRACTION' ?
r_mcbond_it 29 0.523 1.500 ? 'X-RAY DIFFRACTION' ?
r_mcbond_other 12 0.157 1.500 ? 'X-RAY DIFFRACTION' ?
r_mcangle_it 46 0.853 2.000 ? 'X-RAY DIFFRACTION' ?
r_scbond_it 27 1.220 3.000 ? 'X-RAY DIFFRACTION' ?
r_scangle_it 29 1.673 4.500 ? 'X-RAY DIFFRACTION' ?
#
_refine_ls_shell.d_res_high 1.8000
_refine_ls_shell.d_res_low 2.0110
_refine_ls_shell.pdbx_total_number_of_bins_used 5
_refine_ls_shell.percent_reflns_obs 72.2200
_refine_ls_shell.number_reflns_R_work 87
_refine_ls_shell.R_factor_all ?
_refine_ls_shell.R_factor_R_work 0.3820
_refine_ls_shell.R_factor_R_free 0.3300
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free 4
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.number_reflns_all 91
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.redundancy_reflns_obs ?
_refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION'
#
_struct.entry_id 3NVF
_struct.title 'IIHFGS segment 138-143 from human prion'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 3NVF
_struct_keywords.text 'amyloid-like protofibril, PROTEIN FIBRIL'
_struct_keywords.pdbx_keywords 'PROTEIN FIBRIL'
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
#
_struct_ref.id 1
_struct_ref.db_name UNP
_struct_ref.db_code PRIO_HUMAN
_struct_ref.pdbx_db_accession P04156
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code IIHFGS
_struct_ref.pdbx_align_begin 138
_struct_ref.pdbx_db_isoform ?
#
_struct_ref_seq.align_id 1
_struct_ref_seq.ref_id 1
_struct_ref_seq.pdbx_PDB_id_code 3NVF
_struct_ref_seq.pdbx_strand_id A
_struct_ref_seq.seq_align_beg 1
_struct_ref_seq.pdbx_seq_align_beg_ins_code ?
_struct_ref_seq.seq_align_end 6
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession P04156
_struct_ref_seq.db_align_beg 138
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 143
_struct_ref_seq.pdbx_db_align_end_ins_code ?
_struct_ref_seq.pdbx_auth_seq_align_beg 1
_struct_ref_seq.pdbx_auth_seq_align_end 6
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_defined_assembly
_pdbx_struct_assembly.method_details ?
_pdbx_struct_assembly.oligomeric_details decameric
_pdbx_struct_assembly.oligomeric_count 10
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10
_pdbx_struct_assembly_gen.asym_id_list A,B
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
2 'crystal symmetry operation' 1_557 x,y,z+2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 9.6080000000
3 'crystal symmetry operation' 1_556 x,y,z+1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4.8040000000
4 'crystal symmetry operation' 1_554 x,y,z-1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -4.8040000000
5 'crystal symmetry operation' 1_553 x,y,z-2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -9.6080000000
6 'crystal symmetry operation' 2_657 -x+1,-y,z+2 -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 9.6080000000
7 'crystal symmetry operation' 2_656 -x+1,-y,z+1 -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4.8040000000
8 'crystal symmetry operation' 2_655 -x+1,-y,z -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
9 'crystal symmetry operation' 2_654 -x+1,-y,z-1 -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -4.8040000000
10 'crystal symmetry operation' 2_653 -x+1,-y,z-2 -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000
0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -9.6080000000
#
_struct_biol.id 1
_struct_biol.details ?
#
_struct_site.id AC1
_struct_site.pdbx_evidence_code Software
_struct_site.pdbx_auth_asym_id A
_struct_site.pdbx_auth_comp_id MPD
_struct_site.pdbx_auth_seq_id 7
_struct_site.pdbx_auth_ins_code ?
_struct_site.pdbx_num_residues 5
_struct_site.details 'BINDING SITE FOR RESIDUE MPD A 7'
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 5 ILE A 1 ? ILE A 1 . ? 4_444 ?
2 AC1 5 ILE A 2 ? ILE A 2 . ? 4_444 ?
3 AC1 5 HIS A 3 ? HIS A 3 . ? 1_555 ?
4 AC1 5 HIS A 3 ? HIS A 3 . ? 1_554 ?
5 AC1 5 PHE A 4 ? PHE A 4 . ? 3_544 ?
#
_pdbx_phasing_MR.entry_id 3NVF
_pdbx_phasing_MR.method_rotation ?
_pdbx_phasing_MR.method_translation ?
_pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO'
_pdbx_phasing_MR.R_factor ?
_pdbx_phasing_MR.R_rigid_body ?
_pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ?
_pdbx_phasing_MR.correlation_coeff_Io_to_Ic ?
_pdbx_phasing_MR.d_res_high_rotation 2.200
_pdbx_phasing_MR.d_res_low_rotation 20.600
_pdbx_phasing_MR.d_res_high_translation 2.200
_pdbx_phasing_MR.d_res_low_translation 20.600
_pdbx_phasing_MR.packing ?
_pdbx_phasing_MR.reflns_percent_rotation ?
_pdbx_phasing_MR.reflns_percent_translation ?
_pdbx_phasing_MR.sigma_F_rotation ?
_pdbx_phasing_MR.sigma_F_translation ?
_pdbx_phasing_MR.sigma_I_rotation ?
_pdbx_phasing_MR.sigma_I_translation ?
#
_phasing.method MR
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
GLY N N N N 1
GLY CA C N N 2
GLY C C N N 3
GLY O O N N 4
GLY OXT O N N 5
GLY H H N N 6
GLY H2 H N N 7
GLY HA2 H N N 8
GLY HA3 H N N 9
GLY HXT H N N 10
HIS N N N N 11
HIS CA C N S 12
HIS C C N N 13
HIS O O N N 14
HIS CB C N N 15
HIS CG C Y N 16
HIS ND1 N Y N 17
HIS CD2 C Y N 18
HIS CE1 C Y N 19
HIS NE2 N Y N 20
HIS OXT O N N 21
HIS H H N N 22
HIS H2 H N N 23
HIS HA H N N 24
HIS HB2 H N N 25
HIS HB3 H N N 26
HIS HD1 H N N 27
HIS HD2 H N N 28
HIS HE1 H N N 29
HIS HE2 H N N 30
HIS HXT H N N 31
ILE N N N N 32
ILE CA C N S 33
ILE C C N N 34
ILE O O N N 35
ILE CB C N S 36
ILE CG1 C N N 37
ILE CG2 C N N 38
ILE CD1 C N N 39
ILE OXT O N N 40
ILE H H N N 41
ILE H2 H N N 42
ILE HA H N N 43
ILE HB H N N 44
ILE HG12 H N N 45
ILE HG13 H N N 46
ILE HG21 H N N 47
ILE HG22 H N N 48
ILE HG23 H N N 49
ILE HD11 H N N 50
ILE HD12 H N N 51
ILE HD13 H N N 52
ILE HXT H N N 53
MPD C1 C N N 54
MPD C2 C N N 55
MPD O2 O N N 56
MPD CM C N N 57
MPD C3 C N N 58
MPD C4 C N S 59
MPD O4 O N N 60
MPD C5 C N N 61
MPD H11 H N N 62
MPD H12 H N N 63
MPD H13 H N N 64
MPD HO2 H N N 65
MPD HM1 H N N 66
MPD HM2 H N N 67
MPD HM3 H N N 68
MPD H31 H N N 69
MPD H32 H N N 70
MPD H4 H N N 71
MPD HO4 H N N 72
MPD H51 H N N 73
MPD H52 H N N 74
MPD H53 H N N 75
PHE N N N N 76
PHE CA C N S 77
PHE C C N N 78
PHE O O N N 79
PHE CB C N N 80
PHE CG C Y N 81
PHE CD1 C Y N 82
PHE CD2 C Y N 83
PHE CE1 C Y N 84
PHE CE2 C Y N 85
PHE CZ C Y N 86
PHE OXT O N N 87
PHE H H N N 88
PHE H2 H N N 89
PHE HA H N N 90
PHE HB2 H N N 91
PHE HB3 H N N 92
PHE HD1 H N N 93
PHE HD2 H N N 94
PHE HE1 H N N 95
PHE HE2 H N N 96
PHE HZ H N N 97
PHE HXT H N N 98
SER N N N N 99
SER CA C N S 100
SER C C N N 101
SER O O N N 102
SER CB C N N 103
SER OG O N N 104
SER OXT O N N 105
SER H H N N 106
SER H2 H N N 107
SER HA H N N 108
SER HB2 H N N 109
SER HB3 H N N 110
SER HG H N N 111
SER HXT H N N 112
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
GLY N CA sing N N 1
GLY N H sing N N 2
GLY N H2 sing N N 3
GLY CA C sing N N 4
GLY CA HA2 sing N N 5
GLY CA HA3 sing N N 6
GLY C O doub N N 7
GLY C OXT sing N N 8
GLY OXT HXT sing N N 9
HIS N CA sing N N 10
HIS N H sing N N 11
HIS N H2 sing N N 12
HIS CA C sing N N 13
HIS CA CB sing N N 14
HIS CA HA sing N N 15
HIS C O doub N N 16
HIS C OXT sing N N 17
HIS CB CG sing N N 18
HIS CB HB2 sing N N 19
HIS CB HB3 sing N N 20
HIS CG ND1 sing Y N 21
HIS CG CD2 doub Y N 22
HIS ND1 CE1 doub Y N 23
HIS ND1 HD1 sing N N 24
HIS CD2 NE2 sing Y N 25
HIS CD2 HD2 sing N N 26
HIS CE1 NE2 sing Y N 27
HIS CE1 HE1 sing N N 28
HIS NE2 HE2 sing N N 29
HIS OXT HXT sing N N 30
ILE N CA sing N N 31
ILE N H sing N N 32
ILE N H2 sing N N 33
ILE CA C sing N N 34
ILE CA CB sing N N 35
ILE CA HA sing N N 36
ILE C O doub N N 37
ILE C OXT sing N N 38
ILE CB CG1 sing N N 39
ILE CB CG2 sing N N 40
ILE CB HB sing N N 41
ILE CG1 CD1 sing N N 42
ILE CG1 HG12 sing N N 43
ILE CG1 HG13 sing N N 44
ILE CG2 HG21 sing N N 45
ILE CG2 HG22 sing N N 46
ILE CG2 HG23 sing N N 47
ILE CD1 HD11 sing N N 48
ILE CD1 HD12 sing N N 49
ILE CD1 HD13 sing N N 50
ILE OXT HXT sing N N 51
MPD C1 C2 sing N N 52
MPD C1 H11 sing N N 53
MPD C1 H12 sing N N 54
MPD C1 H13 sing N N 55
MPD C2 O2 sing N N 56
MPD C2 CM sing N N 57
MPD C2 C3 sing N N 58
MPD O2 HO2 sing N N 59
MPD CM HM1 sing N N 60
MPD CM HM2 sing N N 61
MPD CM HM3 sing N N 62
MPD C3 C4 sing N N 63
MPD C3 H31 sing N N 64
MPD C3 H32 sing N N 65
MPD C4 O4 sing N N 66
MPD C4 C5 sing N N 67
MPD C4 H4 sing N N 68
MPD O4 HO4 sing N N 69
MPD C5 H51 sing N N 70
MPD C5 H52 sing N N 71
MPD C5 H53 sing N N 72
PHE N CA sing N N 73
PHE N H sing N N 74
PHE N H2 sing N N 75
PHE CA C sing N N 76
PHE CA CB sing N N 77
PHE CA HA sing N N 78
PHE C O doub N N 79
PHE C OXT sing N N 80
PHE CB CG sing N N 81
PHE CB HB2 sing N N 82
PHE CB HB3 sing N N 83
PHE CG CD1 doub Y N 84
PHE CG CD2 sing Y N 85
PHE CD1 CE1 sing Y N 86
PHE CD1 HD1 sing N N 87
PHE CD2 CE2 doub Y N 88
PHE CD2 HD2 sing N N 89
PHE CE1 CZ doub Y N 90
PHE CE1 HE1 sing N N 91
PHE CE2 CZ sing Y N 92
PHE CE2 HE2 sing N N 93
PHE CZ HZ sing N N 94
PHE OXT HXT sing N N 95
SER N CA sing N N 96
SER N H sing N N 97
SER N H2 sing N N 98
SER CA C sing N N 99
SER CA CB sing N N 100
SER CA HA sing N N 101
SER C O doub N N 102
SER C OXT sing N N 103
SER CB OG sing N N 104
SER CB HB2 sing N N 105
SER CB HB3 sing N N 106
SER OG HG sing N N 107
SER OXT HXT sing N N 108
#
_atom_sites.entry_id 3NVF
_atom_sites.fract_transf_matrix[1][1] 0.036303
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.032240
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 0.208160
_atom_sites.fract_transf_vector[1] 0.000000
_atom_sites.fract_transf_vector[2] 0.000000
_atom_sites.fract_transf_vector[3] 0.000000
#
loop_
_atom_type.symbol
C
N
O
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . ILE A 1 1 ? 12.601 -8.390 -1.212 1.00 14.40 ? 1 ILE A N 1
ATOM 2 C CA . ILE A 1 1 ? 11.409 -7.582 -1.598 1.00 14.86 ? 1 ILE A CA 1
ATOM 3 C C . ILE A 1 1 ? 11.447 -6.187 -1.019 1.00 15.15 ? 1 ILE A C 1
ATOM 4 O O . ILE A 1 1 ? 11.624 -6.019 0.184 1.00 15.28 ? 1 ILE A O 1
ATOM 5 C CB . ILE A 1 1 ? 10.071 -8.190 -1.105 1.00 15.06 ? 1 ILE A CB 1
ATOM 6 C CG1 . ILE A 1 1 ? 9.822 -9.555 -1.736 1.00 15.45 ? 1 ILE A CG1 1
ATOM 7 C CG2 . ILE A 1 1 ? 8.896 -7.243 -1.431 1.00 14.46 ? 1 ILE A CG2 1
ATOM 8 C CD1 . ILE A 1 1 ? 8.719 -10.338 -1.060 1.00 13.87 ? 1 ILE A CD1 1
ATOM 9 N N . ILE A 1 2 ? 11.286 -5.195 -1.890 1.00 14.95 ? 2 ILE A N 1
ATOM 10 C CA . ILE A 1 2 ? 10.919 -3.862 -1.487 1.00 15.44 ? 2 ILE A CA 1
ATOM 11 C C . ILE A 1 2 ? 9.523 -3.593 -2.061 1.00 15.35 ? 2 ILE A C 1
ATOM 12 O O . ILE A 1 2 ? 9.338 -3.591 -3.287 1.00 15.42 ? 2 ILE A O 1
ATOM 13 C CB . ILE A 1 2 ? 11.895 -2.801 -2.009 1.00 15.07 ? 2 ILE A CB 1
ATOM 14 C CG1 . ILE A 1 2 ? 13.323 -3.103 -1.584 1.00 15.89 ? 2 ILE A CG1 1
ATOM 15 C CG2 . ILE A 1 2 ? 11.527 -1.437 -1.466 1.00 16.14 ? 2 ILE A CG2 1
ATOM 16 C CD1 . ILE A 1 2 ? 14.311 -2.022 -2.067 1.00 13.94 ? 2 ILE A CD1 1
ATOM 17 N N . HIS A 1 3 ? 8.548 -3.384 -1.170 1.00 15.48 ? 3 HIS A N 1
ATOM 18 C CA . HIS A 1 3 ? 7.157 -3.199 -1.565 1.00 14.66 ? 3 HIS A CA 1
ATOM 19 C C . HIS A 1 3 ? 6.549 -1.944 -0.924 1.00 15.08 ? 3 HIS A C 1
ATOM 20 O O . HIS A 1 3 ? 6.367 -1.847 0.298 1.00 13.92 ? 3 HIS A O 1
ATOM 21 C CB . HIS A 1 3 ? 6.331 -4.446 -1.229 1.00 14.83 ? 3 HIS A CB 1
ATOM 22 C CG . HIS A 1 3 ? 4.904 -4.389 -1.700 1.00 12.74 ? 3 HIS A CG 1
ATOM 23 N ND1 . HIS A 1 3 ? 3.916 -5.168 -1.144 1.00 11.28 ? 3 HIS A ND1 1
ATOM 24 C CD2 . HIS A 1 3 ? 4.297 -3.645 -2.653 1.00 12.74 ? 3 HIS A CD2 1
ATOM 25 C CE1 . HIS A 1 3 ? 2.764 -4.910 -1.730 1.00 10.42 ? 3 HIS A CE1 1
ATOM 26 N NE2 . HIS A 1 3 ? 2.961 -3.974 -2.640 1.00 10.20 ? 3 HIS A NE2 1
ATOM 27 N N . PHE A 1 4 ? 6.233 -0.986 -1.787 1.00 14.93 ? 4 PHE A N 1
ATOM 28 C CA . PHE A 1 4 ? 5.578 0.242 -1.389 1.00 15.32 ? 4 PHE A CA 1
ATOM 29 C C . PHE A 1 4 ? 4.163 0.163 -1.949 1.00 15.08 ? 4 PHE A C 1
ATOM 30 O O . PHE A 1 4 ? 3.922 0.469 -3.112 1.00 15.04 ? 4 PHE A O 1
ATOM 31 C CB . PHE A 1 4 ? 6.349 1.453 -1.920 1.00 15.04 ? 4 PHE A CB 1
ATOM 32 C CG . PHE A 1 4 ? 7.510 1.860 -1.047 1.00 17.30 ? 4 PHE A CG 1
ATOM 33 C CD1 . PHE A 1 4 ? 7.544 3.103 -0.443 1.00 19.00 ? 4 PHE A CD1 1
ATOM 34 C CD2 . PHE A 1 4 ? 8.553 0.994 -0.807 1.00 17.85 ? 4 PHE A CD2 1
ATOM 35 C CE1 . PHE A 1 4 ? 8.611 3.467 0.370 1.00 19.54 ? 4 PHE A CE1 1
ATOM 36 C CE2 . PHE A 1 4 ? 9.614 1.364 -0.001 1.00 18.92 ? 4 PHE A CE2 1
ATOM 37 C CZ . PHE A 1 4 ? 9.641 2.596 0.582 1.00 17.54 ? 4 PHE A CZ 1
ATOM 38 N N . GLY A 1 5 ? 3.245 -0.292 -1.113 1.00 15.28 ? 5 GLY A N 1
ATOM 39 C CA . GLY A 1 5 ? 1.874 -0.538 -1.541 1.00 15.77 ? 5 GLY A CA 1
ATOM 40 C C . GLY A 1 5 ? 1.277 -1.676 -0.760 1.00 16.20 ? 5 GLY A C 1
ATOM 41 O O . GLY A 1 5 ? 1.748 -2.006 0.324 1.00 16.34 ? 5 GLY A O 1
ATOM 42 N N . SER A 1 6 ? 0.247 -2.298 -1.320 1.00 17.20 ? 6 SER A N 1
ATOM 43 C CA . SER A 1 6 ? -0.488 -3.353 -0.621 1.00 17.85 ? 6 SER A CA 1
ATOM 44 C C . SER A 1 6 ? -0.705 -4.607 -1.478 1.00 18.85 ? 6 SER A C 1
ATOM 45 O O . SER A 1 6 ? -0.263 -4.675 -2.638 1.00 19.94 ? 6 SER A O 1
ATOM 46 C CB . SER A 1 6 ? -1.830 -2.804 -0.132 1.00 17.78 ? 6 SER A CB 1
ATOM 47 O OG . SER A 1 6 ? -1.621 -1.788 0.829 1.00 16.74 ? 6 SER A OG 1
ATOM 48 O OXT . SER A 1 6 ? -1.319 -5.592 -1.029 1.00 19.55 ? 6 SER A OXT 1
HETATM 49 C C1 . MPD B 2 . ? 4.495 -8.174 -1.940 1.00 52.17 ? 7 MPD A C1 1
HETATM 50 C C2 . MPD B 2 . ? 4.360 -8.256 -3.445 1.00 51.81 ? 7 MPD A C2 1
HETATM 51 O O2 . MPD B 2 . ? 3.776 -7.016 -3.921 1.00 51.08 ? 7 MPD A O2 1
HETATM 52 C CM . MPD B 2 . ? 5.759 -8.409 -4.028 1.00 51.56 ? 7 MPD A CM 1
HETATM 53 C C3 . MPD B 2 . ? 3.501 -9.464 -3.828 1.00 52.22 ? 7 MPD A C3 1
HETATM 54 C C4 . MPD B 2 . ? 1.977 -9.352 -3.653 1.00 52.51 ? 7 MPD A C4 1
HETATM 55 O O4 . MPD B 2 . ? 1.528 -8.090 -3.199 1.00 52.98 ? 7 MPD A O4 1
HETATM 56 C C5 . MPD B 2 . ? 1.281 -9.668 -4.976 1.00 52.46 ? 7 MPD A C5 1
#