HEADER PROTEIN FIBRIL 09-JAN-20 6VHB
TITLE 1.4A LOW-DOSE STRUCTURE OF GSNQNNF DETERMINED FROM INITIAL PHASES
TITLE 2 GENERATED USING RADIATION DAMAGE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GSNQNNF;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 4 ORGANISM_TAXID: 32630
KEYWDS MICROED, DAMAGE, PHASING, RIP, PROTEIN FIBRIL
EXPDTA ELECTRON CRYSTALLOGRAPHY
AUTHOR M.W.MARTYNOWYCZ,J.HATTNE,T.GONEN
REVDAT 3 06-MAR-24 6VHB 1 REMARK LINK
REVDAT 2 22-APR-20 6VHB 1 JRNL
REVDAT 1 19-FEB-20 6VHB 0
JRNL AUTH M.W.MARTYNOWYCZ,J.HATTNE,T.GONEN
JRNL TITL EXPERIMENTAL PHASING OF MICROED DATA USING RADIATION DAMAGE.
JRNL REF STRUCTURE V. 28 458 2020
JRNL REFN ISSN 0969-2126
JRNL PMID 32023481
JRNL DOI 10.1016/J.STR.2020.01.008
REMARK 2
REMARK 2 RESOLUTION. 1.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELX
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 77.2
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RCOMPLETE RANDOM
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 55
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 5
REMARK 3 SOLVENT ATOMS : 1
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL
REMARK 3 NUMBER OF RESTRAINTS : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 ANGLE DISTANCES (A) : NULL
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6VHB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-20.
REMARK 100 THE DEPOSITION ID IS D_1000246394.
REMARK 240
REMARK 240 EXPERIMENTAL DETAILS
REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY
REMARK 240 SAMPLE TYPE : 3D ARRAY
REMARK 240 SPECIMEN TYPE : NULL
REMARK 240 DATA ACQUISITION
REMARK 240 DATE OF DATA COLLECTION : NULL
REMARK 240 TEMPERATURE (KELVIN) : NULL
REMARK 240 PH : NULL
REMARK 240 NUMBER OF CRYSTALS USED : NULL
REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20
REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K)
REMARK 240 ACCELERATION VOLTAGE (KV) : 200
REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 713
REMARK 240 RESOLUTION RANGE HIGH (A) : 1.400
REMARK 240 RESOLUTION RANGE LOW (A) : NULL
REMARK 240 DATA SCALING SOFTWARE : XSCALE
REMARK 240 COMPLETENESS FOR RANGE (%) : 77.2
REMARK 240 DATA REDUNDANCY : 8.452
REMARK 240 IN THE HIGHEST RESOLUTION SHELL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.40
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.51
REMARK 240 COMPLETENESS FOR SHELL (%) : 78.5
REMARK 240 DATA REDUNDANCY IN SHELL : 8.55
REMARK 240 R MERGE FOR SHELL (I) : 0.26200
REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 240 SOFTWARE USED : NULL
REMARK 240 STARTING MODEL : NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 PHE A 7 CG - CD1 - CE1 ANGL. DEV. = 6.9 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLY A 1 N
REMARK 620 2 GLY A 1 O 85.4
REMARK 620 3 PHE A 7 O 115.0 45.1
REMARK 620 4 ACT A 102 O 146.1 87.4 81.3
REMARK 620 5 ACT A 102 OXT 115.7 97.3 54.5 98.0
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 102
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6CLI RELATED DB: PDB
REMARK 900 ORIGINAL STRUCTURE
REMARK 900 RELATED ID: EMD-21202 RELATED DB: EMDB
REMARK 900 1.4A LOW-DOSE STRUCTURE OF GSNQNNF DETERMINED FROM INITIAL PHASES
REMARK 900 GENERATED USING RADIATION DAMAGE
DBREF 6VHB A 1 7 PDB 6VHB 6VHB 1 7
SEQRES 1 A 7 GLY SER ASN GLN ASN ASN PHE
HET ZN A 101 1
HET ACT A 102 4
HETNAM ZN ZINC ION
HETNAM ACT ACETATE ION
FORMUL 2 ZN ZN 2+
FORMUL 3 ACT C2 H3 O2 1-
FORMUL 4 HOH *(H2 O)
LINK N GLY A 1 ZN ZN A 101 1555 1555 1.98
LINK O GLY A 1 ZN ZN A 101 1555 1555 1.86
LINK O PHE A 7 ZN ZN A 101 1555 1644 2.09
LINK ZN ZN A 101 O ACT A 102 1555 1555 2.05
LINK ZN ZN A 101 OXT ACT A 102 1555 1655 2.03
SITE 1 AC1 2 GLY A 1 ACT A 102
SITE 1 AC2 2 GLY A 1 ZN A 101
CRYST1 4.880 14.170 17.620 83.60 84.98 83.31 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.204918 -0.024036 -0.015622 0.00000
SCALE2 0.000000 0.071055 -0.007312 0.00000
SCALE3 0.000000 0.000000 0.057273 0.00000
ATOM 1 N GLY A 1 3.399 30.601 19.375 1.00 0.93 N
ATOM 2 CA GLY A 1 3.623 30.787 17.936 1.00 2.92 C
ATOM 3 C GLY A 1 2.760 29.752 17.177 1.00 2.30 C
ATOM 4 O GLY A 1 2.082 28.974 17.829 1.00 1.80 O
ATOM 5 N SER A 2 2.858 29.801 15.858 1.00 0.08 N
ATOM 6 CA SER A 2 1.978 28.995 15.000 1.00 0.69 C
ATOM 7 C SER A 2 2.692 27.753 14.486 1.00 0.08 C
ATOM 8 O SER A 2 3.941 27.738 14.345 1.00 5.90 O
ATOM 9 CB SER A 2 1.496 29.908 13.854 1.00 0.08 C
ATOM 10 OG SER A 2 0.525 30.854 14.292 1.00 1.15 O
ATOM 11 N ASN A 3 2.001 26.639 14.227 1.00 3.22 N
ATOM 12 CA ASN A 3 2.564 25.333 13.879 1.00 0.71 C
ATOM 13 C ASN A 3 1.886 24.766 12.635 1.00 5.01 C
ATOM 14 O ASN A 3 0.664 24.755 12.452 1.00 2.18 O
ATOM 15 CB ASN A 3 2.476 24.373 15.080 1.00 1.83 C
ATOM 16 CG ASN A 3 3.085 24.989 16.330 1.00 2.00 C
ATOM 17 OD1 ASN A 3 4.269 24.769 16.627 1.00 9.96 O
ATOM 18 ND2 ASN A 3 2.316 25.785 17.055 1.00 5.13 N
ATOM 19 N GLN A 4 2.678 24.238 11.700 1.00 4.45 N
ATOM 20 CA GLN A 4 2.184 23.550 10.509 1.00 3.39 C
ATOM 21 C GLN A 4 2.899 22.223 10.328 1.00 2.04 C
ATOM 22 O GLN A 4 4.140 22.071 10.430 1.00 0.12 O
ATOM 23 CB GLN A 4 2.369 24.421 9.272 1.00 6.63 C
ATOM 24 CG GLN A 4 1.691 23.888 8.022 1.00 1.39 C
ATOM 25 CD GLN A 4 1.991 24.745 6.803 1.00 4.34 C
ATOM 26 OE1 GLN A 4 3.183 24.831 6.461 1.00 3.23 O
ATOM 27 NE2 GLN A 4 1.043 25.357 6.123 1.00 0.45 N
ATOM 28 N ASN A 5 2.112 21.173 10.084 1.00 0.09 N
ATOM 29 CA ASN A 5 2.651 19.846 9.815 1.00 2.42 C
ATOM 30 C ASN A 5 2.254 19.479 8.384 1.00 0.08 C
ATOM 31 O ASN A 5 1.039 19.403 8.168 1.00 2.03 O
ATOM 32 CB ASN A 5 2.134 18.813 10.809 1.00 3.76 C
ATOM 33 CG ASN A 5 2.548 18.996 12.249 1.00 3.78 C
ATOM 34 OD1 ASN A 5 3.731 18.787 12.574 1.00 6.41 O
ATOM 35 ND2 ASN A 5 1.663 19.359 13.159 1.00 6.64 N
ATOM 36 N ASN A 6 3.197 19.266 7.485 1.00 5.08 N
ATOM 37 CA ASN A 6 2.922 18.857 6.113 1.00 0.40 C
ATOM 38 C ASN A 6 3.395 17.427 5.919 1.00 0.08 C
ATOM 39 O ASN A 6 4.578 17.213 5.622 1.00 0.08 O
ATOM 40 CB ASN A 6 3.595 19.774 5.086 1.00 0.71 C
ATOM 41 CG ASN A 6 3.264 21.223 5.407 1.00 1.54 C
ATOM 42 OD1 ASN A 6 4.162 22.031 5.685 1.00 0.08 O
ATOM 43 ND2 ASN A 6 1.990 21.560 5.360 1.00 6.19 N
ATOM 44 N PHE A 7 2.564 16.413 6.100 1.00 0.08 N
ATOM 45 CA PHE A 7 2.941 15.023 5.907 1.00 0.08 C
ATOM 46 C PHE A 7 3.109 14.697 4.440 1.00 0.79 C
ATOM 47 O PHE A 7 3.786 13.632 4.230 1.00 5.35 O
ATOM 48 CB PHE A 7 1.846 14.141 6.527 1.00 0.08 C
ATOM 49 CG PHE A 7 1.860 14.227 8.026 1.00 0.90 C
ATOM 50 CD1 PHE A 7 2.665 13.471 8.827 1.00 0.08 C
ATOM 51 CD2 PHE A 7 1.035 15.165 8.667 1.00 1.31 C
ATOM 52 CE1 PHE A 7 2.732 13.481 10.201 1.00 0.08 C
ATOM 53 CE2 PHE A 7 1.073 15.196 10.044 1.00 0.08 C
ATOM 54 CZ PHE A 7 1.913 14.429 10.837 1.00 4.13 C
ATOM 55 OXT PHE A 7 2.697 15.269 3.478 1.00 3.61 O
TER 56 PHE A 7
HETATM 57 ZN ZN A 101 2.274 28.998 19.674 1.00 3.34 ZN
HETATM 58 C ACT A 102 -0.344 27.222 20.022 1.00 9.18 C
HETATM 59 O ACT A 102 0.367 28.256 19.789 1.00 0.08 O
HETATM 60 OXT ACT A 102 -1.608 27.244 19.853 1.00 4.95 O
HETATM 61 CH3 ACT A 102 0.296 25.894 20.494 1.00 4.49 C
HETATM 62 O HOH A 201 5.941 17.825 3.335 1.00 6.22 O
CONECT 1 57
CONECT 4 57
CONECT 57 1 4 59
CONECT 58 59 60 61
CONECT 59 57 58
CONECT 60 58
CONECT 61 58
MASTER 184 0 2 0 0 0 2 6 61 1 7 1
END