data_3DG1
#
_entry.id 3DG1
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.389
_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 3DG1 pdb_00003dg1 10.2210/pdb3dg1/pdb
RCSB RCSB047992 ? ?
WWPDB D_1000047992 ? ?
#
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 2008-07-01
2 'Structure model' 1 1 2011-07-13
3 'Structure model' 1 2 2015-06-03
4 'Structure model' 1 3 2017-10-25
5 'Structure model' 1 4 2024-02-21
6 'Structure model' 1 5 2024-04-03
#
_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' 'Derived calculations'
3 4 'Structure model' 'Refinement description'
4 5 'Structure model' 'Data collection'
5 5 'Structure model' 'Database references'
6 6 'Structure model' 'Refinement description'
#
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 4 'Structure model' software
2 5 'Structure model' chem_comp_atom
3 5 'Structure model' chem_comp_bond
4 5 'Structure model' database_2
5 6 'Structure model' pdbx_initial_refinement_model
#
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 5 'Structure model' '_database_2.pdbx_DOI'
2 5 'Structure model' '_database_2.pdbx_database_accession'
#
_pdbx_database_status.entry_id 3DG1
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.recvd_initial_deposition_date 2008-06-12
_pdbx_database_status.status_code REL
_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.methods_development_category ?
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_nmr_data ?
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.db_id
_pdbx_database_related.details
_pdbx_database_related.content_type
PDB 1YJO . unspecified
PDB 2OMM . unspecified
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Wiltzius, J.J.' 1
'Sievers, S.A.' 2
'Sawaya, M.R.' 3
'Cascio, D.' 4
'Eisenberg, D.' 5
#
_citation.id primary
_citation.title 'Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin).'
_citation.journal_abbrev 'Protein Sci.'
_citation.journal_volume 17
_citation.page_first 1467
_citation.page_last 1474
_citation.year 2008
_citation.journal_id_ASTM PRCIEI
_citation.country US
_citation.journal_id_ISSN 0961-8368
_citation.journal_id_CSD 0795
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 18556473
_citation.pdbx_database_id_DOI 10.1110/ps.036509.108
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Wiltzius, J.J.' 1 ?
primary 'Sievers, S.A.' 2 ?
primary 'Sawaya, M.R.' 3 ?
primary 'Cascio, D.' 4 ?
primary 'Popov, D.' 5 ?
primary 'Riekel, C.' 6 ?
primary 'Eisenberg, D.' 7 ?
#
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 'SSTNVG from Islet Amyloid Polypeptide' 563.560 1 ? ? ? ?
2 water nat water 18.015 2 ? ? ? ?
#
_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 SSTNVG
_entity_poly.pdbx_seq_one_letter_code_can SSTNVG
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
_pdbx_entity_nonpoly.entity_id 2
_pdbx_entity_nonpoly.name water
_pdbx_entity_nonpoly.comp_id HOH
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 SER n
1 2 SER n
1 3 THR n
1 4 ASN n
1 5 VAL n
1 6 GLY n
#
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
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118
GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067
HOH non-polymer . WATER ? 'H2 O' 18.015
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119
VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146
#
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 SER 1 1 1 SER SER A . n
A 1 2 SER 2 2 2 SER SER A . n
A 1 3 THR 3 3 3 THR THR A . n
A 1 4 ASN 4 4 4 ASN ASN A . n
A 1 5 VAL 5 5 5 VAL VAL A . n
A 1 6 GLY 6 6 6 GLY GLY A . n
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 HOH 1 7 1 HOH HOH A .
B 2 HOH 2 8 2 HOH HOH A .
#
loop_
_software.name
_software.version
_software.date
_software.type
_software.contact_author
_software.contact_author_email
_software.classification
_software.location
_software.language
_software.citation_id
_software.pdbx_ordinal
DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction'
http://www.hkl-xray.com/ ? ? 1
SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling'
http://www.hkl-xray.com/ ? ? 2
PHASER . ? program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing
http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 3
REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement
http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4
PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction'
http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5
#
_cell.length_a 41.400
_cell.length_b 4.785
_cell.length_c 18.594
_cell.angle_alpha 90.000
_cell.angle_beta 115.880
_cell.angle_gamma 90.000
_cell.entry_id 3DG1
_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 'C 1 2 1'
_symmetry.entry_id 3DG1
_symmetry.Int_Tables_number 5
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.space_group_name_Hall ?
#
_exptl.crystals_number 1
_exptl.entry_id 3DG1
_exptl.method 'X-RAY DIFFRACTION'
#
_exptl_crystal.id 1
_exptl_crystal.density_Matthews ?
_exptl_crystal.density_meas ?
_exptl_crystal.density_percent_sol ?
_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 ?
_exptl_crystal_grow.temp 293
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pdbx_details '30% MPD, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K'
_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 'MARMOSAIC 225 mm CCD'
_diffrn_detector.pdbx_collection_date 2007-07-21
_diffrn_detector.details ?
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.monochromator 'Si(111) monochromator'
_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 1.0
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source SYNCHROTRON
_diffrn_source.type 'SLS BEAMLINE X06SA'
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 1.0
_diffrn_source.pdbx_synchrotron_site SLS
_diffrn_source.pdbx_synchrotron_beamline X06SA
#
_reflns.entry_id 3DG1
_reflns.d_resolution_high 1.650
_reflns.d_resolution_low 90.000
_reflns.number_obs 460
_reflns.pdbx_Rmerge_I_obs 0.170
_reflns.pdbx_netI_over_sigmaI 5.500
_reflns.pdbx_chi_squared 1.472
_reflns.pdbx_redundancy 2.800
_reflns.percent_possible_obs 97.900
_reflns.observed_criterion_sigma_F 0
_reflns.observed_criterion_sigma_I 0
_reflns.number_all 460
_reflns.pdbx_Rsym_value ?
_reflns.B_iso_Wilson_estimate 30.7
_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_ordinal 1
_reflns.pdbx_diffrn_id 1
#
_reflns_shell.d_res_high 1.65
_reflns_shell.d_res_low 1.71
_reflns_shell.number_measured_obs ?
_reflns_shell.number_measured_all ?
_reflns_shell.number_unique_obs ?
_reflns_shell.Rmerge_I_obs .524
_reflns_shell.meanI_over_sigI_obs ?
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.pdbx_chi_squared 1.426
_reflns_shell.pdbx_redundancy 3.10
_reflns_shell.percent_possible_obs ?
_reflns_shell.number_unique_all 37
_reflns_shell.percent_possible_all 97.40
_reflns_shell.pdbx_ordinal 1
_reflns_shell.pdbx_diffrn_id 1
#
_refine.entry_id 3DG1
_refine.ls_d_res_high 1.660
_refine.ls_d_res_low 18.620
_refine.pdbx_ls_sigma_F 0.00
_refine.ls_percent_reflns_obs 95.620
_refine.ls_number_reflns_obs 459
_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_obs 0.211
_refine.ls_R_factor_R_work 0.207
_refine.ls_R_factor_R_free 0.244
_refine.ls_percent_reflns_R_free 9.800
_refine.ls_number_reflns_R_free 45
_refine.B_iso_mean 19.277
_refine.aniso_B[1][1] 0.050
_refine.aniso_B[2][2] -0.920
_refine.aniso_B[3][3] 0.730
_refine.aniso_B[1][2] 0.000
_refine.aniso_B[1][3] -0.170
_refine.aniso_B[2][3] 0.000
_refine.correlation_coeff_Fo_to_Fc 0.967
_refine.correlation_coeff_Fo_to_Fc_free 0.960
_refine.pdbx_overall_ESU_R 0.146
_refine.pdbx_overall_ESU_R_Free 0.134
_refine.overall_SU_ML 0.077
_refine.overall_SU_B 2.359
_refine.solvent_model_details MASK
_refine.pdbx_solvent_vdw_probe_radii 1.400
_refine.pdbx_solvent_ion_probe_radii 0.800
_refine.pdbx_solvent_shrinkage_radii 0.800
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD'
_refine.overall_FOM_work_R_set 0.826
_refine.B_iso_max 37.16
_refine.B_iso_min 14.55
_refine.occupancy_max 1.00
_refine.occupancy_min 0.50
_refine.pdbx_ls_sigma_I ?
_refine.ls_number_reflns_all 459
_refine.ls_R_factor_all ?
_refine.ls_redundancy_reflns_obs ?
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.pdbx_starting_model 'poly-alanine beta strand'
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.pdbx_isotropic_thermal_model ?
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.overall_FOM_free_R_set ?
_refine.pdbx_overall_phase_error ?
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_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 39
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 0
_refine_hist.number_atoms_solvent 2
_refine_hist.number_atoms_total 41
_refine_hist.d_res_high 1.660
_refine_hist.d_res_low 18.620
#
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 38 0.006 0.021 ? 'X-RAY DIFFRACTION' ?
r_bond_other_d 20 0.002 0.020 ? 'X-RAY DIFFRACTION' ?
r_angle_refined_deg 51 1.011 1.967 ? 'X-RAY DIFFRACTION' ?
r_angle_other_deg 51 0.455 3.000 ? 'X-RAY DIFFRACTION' ?
r_dihedral_angle_1_deg 5 4.208 5.000 ? 'X-RAY DIFFRACTION' ?
r_dihedral_angle_2_deg 1 75.296 30.000 ? 'X-RAY DIFFRACTION' ?
r_dihedral_angle_3_deg 5 2.845 15.000 ? 'X-RAY DIFFRACTION' ?
r_chiral_restr 7 0.057 0.200 ? 'X-RAY DIFFRACTION' ?
r_gen_planes_refined 43 0.003 0.020 ? 'X-RAY DIFFRACTION' ?
r_gen_planes_other 5 0.000 0.020 ? 'X-RAY DIFFRACTION' ?
r_nbd_refined 1 0.016 0.200 ? 'X-RAY DIFFRACTION' ?
r_nbd_other 11 0.217 0.200 ? 'X-RAY DIFFRACTION' ?
r_nbtor_refined 17 0.156 0.200 ? 'X-RAY DIFFRACTION' ?
r_nbtor_other 25 0.082 0.200 ? 'X-RAY DIFFRACTION' ?
r_symmetry_vdw_refined 4 0.076 0.200 ? 'X-RAY DIFFRACTION' ?
r_symmetry_vdw_other 7 0.286 0.200 ? 'X-RAY DIFFRACTION' ?
r_symmetry_hbond_refined 3 0.114 0.200 ? 'X-RAY DIFFRACTION' ?
r_mcbond_it 38 1.634 2.000 ? 'X-RAY DIFFRACTION' ?
r_mcbond_other 12 0.361 2.000 ? 'X-RAY DIFFRACTION' ?
r_mcangle_it 46 2.248 3.000 ? 'X-RAY DIFFRACTION' ?
r_scbond_it 9 1.451 2.000 ? 'X-RAY DIFFRACTION' ?
r_scangle_it 5 1.458 3.000 ? 'X-RAY DIFFRACTION' ?
#
_refine_ls_shell.d_res_high 1.66
_refine_ls_shell.d_res_low 1.699
_refine_ls_shell.pdbx_total_number_of_bins_used 20
_refine_ls_shell.percent_reflns_obs 69.440
_refine_ls_shell.number_reflns_R_work 25
_refine_ls_shell.R_factor_all ?
_refine_ls_shell.R_factor_R_work 0.379
_refine_ls_shell.R_factor_R_free ?
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free ?
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.redundancy_reflns_obs ?
_refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION'
#
_struct.entry_id 3DG1
_struct.title 'Segment SSTNVG derived from IAPP'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag N
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 3DG1
_struct_keywords.pdbx_keywords 'PROTEIN FIBRIL'
_struct_keywords.text 'steric zipper, IAPP, SSTNVG, Amyloid, 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 PDB
_struct_ref.db_code 3DG1
_struct_ref.pdbx_db_accession 3DG1
_struct_ref.entity_id 1
_struct_ref.pdbx_align_begin ?
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_db_isoform ?
#
_struct_ref_seq.align_id 1
_struct_ref_seq.ref_id 1
_struct_ref_seq.pdbx_PDB_id_code 3DG1
_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 3DG1
_struct_ref_seq.db_align_beg 1
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 6
_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_and_software_defined_assembly
_pdbx_struct_assembly.method_details PISA
_pdbx_struct_assembly.oligomeric_details hexameric
_pdbx_struct_assembly.oligomeric_count 6
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6
_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_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
1.0000000000 0.0000000000 4.7850000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
3 'crystal symmetry operation' 1_575 x,y+2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
1.0000000000 0.0000000000 9.5700000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000
4 'crystal symmetry operation' 4_556 -x+1/2,y+1/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 12.5839466489 0.0000000000
1.0000000000 0.0000000000 2.3925000000 0.0000000000 0.0000000000 -1.0000000000 16.7292113981
5 'crystal symmetry operation' 4_566 -x+1/2,y+3/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 12.5839466489 0.0000000000
1.0000000000 0.0000000000 7.1775000000 0.0000000000 0.0000000000 -1.0000000000 16.7292113981
6 'crystal symmetry operation' 4_576 -x+1/2,y+5/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 12.5839466489 0.0000000000
1.0000000000 0.0000000000 11.9625000000 0.0000000000 0.0000000000 -1.0000000000 16.7292113981
#
_struct_biol.id 1
_struct_biol.details
;The biologic assembly is an amyloid-like fiber that can be generated by multiple application of the symmetry operators X, Y+n, Z and
1/2-X,n+(1/2)+Y,-Z+1, where n is an integer.
;
#
_pdbx_struct_special_symmetry.id 1
_pdbx_struct_special_symmetry.PDB_model_num 1
_pdbx_struct_special_symmetry.auth_asym_id A
_pdbx_struct_special_symmetry.auth_comp_id HOH
_pdbx_struct_special_symmetry.auth_seq_id 7
_pdbx_struct_special_symmetry.PDB_ins_code ?
_pdbx_struct_special_symmetry.label_asym_id B
_pdbx_struct_special_symmetry.label_comp_id HOH
_pdbx_struct_special_symmetry.label_seq_id .
#
_pdbx_phasing_MR.entry_id 3DG1
_pdbx_phasing_MR.method_rotation ?
_pdbx_phasing_MR.method_translation ?
_pdbx_phasing_MR.model_details ?
_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 ?
_pdbx_phasing_MR.d_res_low_rotation ?
_pdbx_phasing_MR.d_res_high_translation ?
_pdbx_phasing_MR.d_res_low_translation ?
_pdbx_phasing_MR.packing 0.000
_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
ASN N N N N 1
ASN CA C N S 2
ASN C C N N 3
ASN O O N N 4
ASN CB C N N 5
ASN CG C N N 6
ASN OD1 O N N 7
ASN ND2 N N N 8
ASN OXT O N N 9
ASN H H N N 10
ASN H2 H N N 11
ASN HA H N N 12
ASN HB2 H N N 13
ASN HB3 H N N 14
ASN HD21 H N N 15
ASN HD22 H N N 16
ASN HXT H N N 17
GLY N N N N 18
GLY CA C N N 19
GLY C C N N 20
GLY O O N N 21
GLY OXT O N N 22
GLY H H N N 23
GLY H2 H N N 24
GLY HA2 H N N 25
GLY HA3 H N N 26
GLY HXT H N N 27
HOH O O N N 28
HOH H1 H N N 29
HOH H2 H N N 30
SER N N N N 31
SER CA C N S 32
SER C C N N 33
SER O O N N 34
SER CB C N N 35
SER OG O N N 36
SER OXT O N N 37
SER H H N N 38
SER H2 H N N 39
SER HA H N N 40
SER HB2 H N N 41
SER HB3 H N N 42
SER HG H N N 43
SER HXT H N N 44
THR N N N N 45
THR CA C N S 46
THR C C N N 47
THR O O N N 48
THR CB C N R 49
THR OG1 O N N 50
THR CG2 C N N 51
THR OXT O N N 52
THR H H N N 53
THR H2 H N N 54
THR HA H N N 55
THR HB H N N 56
THR HG1 H N N 57
THR HG21 H N N 58
THR HG22 H N N 59
THR HG23 H N N 60
THR HXT H N N 61
VAL N N N N 62
VAL CA C N S 63
VAL C C N N 64
VAL O O N N 65
VAL CB C N N 66
VAL CG1 C N N 67
VAL CG2 C N N 68
VAL OXT O N N 69
VAL H H N N 70
VAL H2 H N N 71
VAL HA H N N 72
VAL HB H N N 73
VAL HG11 H N N 74
VAL HG12 H N N 75
VAL HG13 H N N 76
VAL HG21 H N N 77
VAL HG22 H N N 78
VAL HG23 H N N 79
VAL HXT H N N 80
#
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
ASN N CA sing N N 1
ASN N H sing N N 2
ASN N H2 sing N N 3
ASN CA C sing N N 4
ASN CA CB sing N N 5
ASN CA HA sing N N 6
ASN C O doub N N 7
ASN C OXT sing N N 8
ASN CB CG sing N N 9
ASN CB HB2 sing N N 10
ASN CB HB3 sing N N 11
ASN CG OD1 doub N N 12
ASN CG ND2 sing N N 13
ASN ND2 HD21 sing N N 14
ASN ND2 HD22 sing N N 15
ASN OXT HXT sing N N 16
GLY N CA sing N N 17
GLY N H sing N N 18
GLY N H2 sing N N 19
GLY CA C sing N N 20
GLY CA HA2 sing N N 21
GLY CA HA3 sing N N 22
GLY C O doub N N 23
GLY C OXT sing N N 24
GLY OXT HXT sing N N 25
HOH O H1 sing N N 26
HOH O H2 sing N N 27
SER N CA sing N N 28
SER N H sing N N 29
SER N H2 sing N N 30
SER CA C sing N N 31
SER CA CB sing N N 32
SER CA HA sing N N 33
SER C O doub N N 34
SER C OXT sing N N 35
SER CB OG sing N N 36
SER CB HB2 sing N N 37
SER CB HB3 sing N N 38
SER OG HG sing N N 39
SER OXT HXT sing N N 40
THR N CA sing N N 41
THR N H sing N N 42
THR N H2 sing N N 43
THR CA C sing N N 44
THR CA CB sing N N 45
THR CA HA sing N N 46
THR C O doub N N 47
THR C OXT sing N N 48
THR CB OG1 sing N N 49
THR CB CG2 sing N N 50
THR CB HB sing N N 51
THR OG1 HG1 sing N N 52
THR CG2 HG21 sing N N 53
THR CG2 HG22 sing N N 54
THR CG2 HG23 sing N N 55
THR OXT HXT sing N N 56
VAL N CA sing N N 57
VAL N H sing N N 58
VAL N H2 sing N N 59
VAL CA C sing N N 60
VAL CA CB sing N N 61
VAL CA HA sing N N 62
VAL C O doub N N 63
VAL C OXT sing N N 64
VAL CB CG1 sing N N 65
VAL CB CG2 sing N N 66
VAL CB HB sing N N 67
VAL CG1 HG11 sing N N 68
VAL CG1 HG12 sing N N 69
VAL CG1 HG13 sing N N 70
VAL CG2 HG21 sing N N 71
VAL CG2 HG22 sing N N 72
VAL CG2 HG23 sing N N 73
VAL OXT HXT sing N N 74
#
_pdbx_initial_refinement_model.accession_code ?
_pdbx_initial_refinement_model.id 1
_pdbx_initial_refinement_model.entity_id_list ?
_pdbx_initial_refinement_model.type 'in silico model'
_pdbx_initial_refinement_model.source_name Other
_pdbx_initial_refinement_model.details 'poly-alanine beta strand'
#
_atom_sites.entry_id 3DG1
_atom_sites.fract_transf_matrix[1][1] 0.024155
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.011719
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.208986
_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] 0.059777
_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 . SER A 1 1 ? -0.946 0.249 6.730 1.00 19.93 ? 1 SER A N 1
ATOM 2 C CA . SER A 1 1 ? 0.254 -0.325 6.062 1.00 20.07 ? 1 SER A CA 1
ATOM 3 C C . SER A 1 1 ? 1.519 0.418 6.466 1.00 18.61 ? 1 SER A C 1
ATOM 4 O O . SER A 1 1 ? 1.491 1.616 6.723 1.00 15.83 ? 1 SER A O 1
ATOM 5 C CB . SER A 1 1 ? 0.103 -0.272 4.544 1.00 22.06 ? 1 SER A CB 1
ATOM 6 O OG . SER A 1 1 ? -0.040 1.059 4.116 1.00 24.22 ? 1 SER A OG 1
ATOM 7 N N . SER A 1 2 ? 2.626 -0.312 6.544 1.00 19.61 ? 2 SER A N 1
ATOM 8 C CA . SER A 1 2 ? 3.918 0.295 6.833 1.00 18.37 ? 2 SER A CA 1
ATOM 9 C C . SER A 1 2 ? 4.955 -0.315 5.910 1.00 17.46 ? 2 SER A C 1
ATOM 10 O O . SER A 1 2 ? 4.947 -1.524 5.681 1.00 19.22 ? 2 SER A O 1
ATOM 11 C CB . SER A 1 2 ? 4.329 0.061 8.284 1.00 18.73 ? 2 SER A CB 1
ATOM 12 O OG . SER A 1 2 ? 5.563 0.707 8.563 1.00 20.39 ? 2 SER A OG 1
ATOM 13 N N . THR A 1 3 ? 5.843 0.523 5.381 1.00 18.15 ? 3 THR A N 1
ATOM 14 C CA . THR A 1 3 ? 6.911 0.054 4.512 1.00 16.67 ? 3 THR A CA 1
ATOM 15 C C . THR A 1 3 ? 8.231 0.679 4.950 1.00 15.22 ? 3 THR A C 1
ATOM 16 O O . THR A 1 3 ? 8.305 1.880 5.156 1.00 16.42 ? 3 THR A O 1
ATOM 17 C CB . THR A 1 3 ? 6.651 0.418 3.039 1.00 18.67 ? 3 THR A CB 1
ATOM 18 O OG1 . THR A 1 3 ? 5.412 -0.169 2.615 1.00 17.78 ? 3 THR A OG1 1
ATOM 19 C CG2 . THR A 1 3 ? 7.789 -0.070 2.147 1.00 16.93 ? 3 THR A CG2 1
ATOM 20 N N . ASN A 1 4 ? 9.246 -0.158 5.125 1.00 16.77 ? 4 ASN A N 1
ATOM 21 C CA . ASN A 1 4 ? 10.594 0.313 5.423 1.00 16.31 ? 4 ASN A CA 1
ATOM 22 C C . ASN A 1 4 ? 11.565 -0.290 4.422 1.00 16.77 ? 4 ASN A C 1
ATOM 23 O O . ASN A 1 4 ? 11.541 -1.499 4.183 1.00 17.79 ? 4 ASN A O 1
ATOM 24 C CB . ASN A 1 4 ? 11.046 -0.099 6.812 1.00 14.84 ? 4 ASN A CB 1
ATOM 25 C CG . ASN A 1 4 ? 12.385 0.505 7.175 1.00 15.90 ? 4 ASN A CG 1
ATOM 26 O OD1 . ASN A 1 4 ? 12.469 1.694 7.465 1.00 16.72 ? 4 ASN A OD1 1
ATOM 27 N ND2 . ASN A 1 4 ? 13.442 -0.308 7.143 1.00 17.03 ? 4 ASN A ND2 1
ATOM 28 N N . VAL A 1 5 ? 12.402 0.559 3.840 1.00 16.46 ? 5 VAL A N 1
ATOM 29 C CA . VAL A 1 5 ? 13.469 0.117 2.956 1.00 16.12 ? 5 VAL A CA 1
ATOM 30 C C . VAL A 1 5 ? 14.752 0.793 3.408 1.00 17.51 ? 5 VAL A C 1
ATOM 31 O O . VAL A 1 5 ? 14.882 1.995 3.276 1.00 18.49 ? 5 VAL A O 1
ATOM 32 C CB . VAL A 1 5 ? 13.205 0.465 1.483 1.00 16.55 ? 5 VAL A CB 1
ATOM 33 C CG1 . VAL A 1 5 ? 14.374 -0.010 0.630 1.00 15.74 ? 5 VAL A CG1 1
ATOM 34 C CG2 . VAL A 1 5 ? 11.894 -0.170 1.006 1.00 14.55 ? 5 VAL A CG2 1
ATOM 35 N N . GLY A 1 6 ? 15.682 0.015 3.962 1.00 19.94 ? 6 GLY A N 1
ATOM 36 C CA . GLY A 1 6 ? 16.968 0.550 4.416 1.00 21.24 ? 6 GLY A CA 1
ATOM 37 C C . GLY A 1 6 ? 17.447 -0.138 5.672 1.00 24.36 ? 6 GLY A C 1
ATOM 38 O O . GLY A 1 6 ? 16.751 -0.995 6.221 1.00 27.23 ? 6 GLY A O 1
ATOM 39 O OXT . GLY A 1 6 ? 18.536 0.144 6.172 1.00 24.96 ? 6 GLY A OXT 1
HETATM 40 O O . HOH B 2 . ? 16.644 2.271 8.365 0.50 33.57 ? 7 HOH A O 1
HETATM 41 O O . HOH B 2 . ? 3.536 1.874 3.265 1.00 37.16 ? 8 HOH A O 1
#