Header list of 6gat.pdb file
Complete list - 3 20 Bytes
HEADER TRANSCRIPTION/DNA 07-NOV-97 6GAT
TITLE SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA
TITLE 2 COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, REGULARIZED MEAN
TITLE 3 STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3');
COMPND 3 CHAIN: B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*AP*CP*TP*G)-3');
COMPND 7 CHAIN: C;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: NITROGEN REGULATORY PROTEIN AREA;
COMPND 11 CHAIN: A;
COMPND 12 FRAGMENT: DNA BINDING DOMAIN;
COMPND 13 ENGINEERED: YES;
COMPND 14 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES;
SOURCE 5 MOL_ID: 3;
SOURCE 6 ORGANISM_SCIENTIFIC: EMERICELLA NIDULANS;
SOURCE 7 ORGANISM_TAXID: 162425;
SOURCE 8 GENE: POTENTIAL;
SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS DNA BINDING PROTEIN, TRANSCRIPTION FACTOR, ZINC BINDING DOMAIN,
KEYWDS 2 COMPLEX (TRANSCRIPTION REGULATION-DNA), TRANSCRIPTION-DNA COMPLEX
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,M.STARICH,M.WIKSTROM,A.M.GRONENBORN
REVDAT 4 03-NOV-21 6GAT 1 REMARK SEQADV LINK
REVDAT 3 24-FEB-09 6GAT 1 VERSN
REVDAT 2 01-APR-03 6GAT 1 JRNL
REVDAT 1 28-JAN-98 6GAT 0
JRNL AUTH M.R.STARICH,M.WIKSTROM,S.SCHUMACHER,H.N.ARST JR.,
JRNL AUTH 2 A.M.GRONENBORN,G.M.CLORE
JRNL TITL THE SOLUTION STRUCTURE OF THE LEU22-->VAL MUTANT AREA DNA
JRNL TITL 2 BINDING DOMAIN COMPLEXED WITH A TGATAG CORE ELEMENT DEFINES
JRNL TITL 3 A ROLE FOR HYDROPHOBIC PACKING IN THE DETERMINATION OF
JRNL TITL 4 SPECIFICITY.
JRNL REF J.MOL.BIOL. V. 277 621 1998
JRNL REFN ISSN 0022-2836
JRNL PMID 9533884
JRNL DOI 10.1006/JMBI.1997.1626
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES WERE CALCULATED USING THE SIMULATED
REMARK 3 ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT.
REMARK 3 229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING
REMARK 3 THE PROGRAM X-PLOR MODIFIED TO INCORPORATE COUPLING
REMARK 3 CONSTANT RESTRAINTS (GARRETT ET AL. (1994) J. MAGN RESON.
REMARK 3 SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT RESTRAINTS
REMARK 3 (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92
REMARK 3 - 96) RESTRAINTS, DIPOLAR COUPLING RESTRAINTS (TJANDRA ET
REMARK 3 AL. (1997) NATURE STRUCT BIOL 4, 732-738) AND A
REMARK 3 CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC
REMARK 3 ACIDS (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - 1080
REMARK 3 AND (1997) J. MAGN. RESON. 125, 171-177)
REMARK 3
REMARK 3 THE 3D STRUCTURE OF THE COMPLEX OF THE LEU22VAL AREA
REMARK 3 DBD-DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL
REMARK 3 HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON THE
REMARK 3 FOLLOWING 1128 EXPERIMENTAL RESTRAINTS
REMARK 3
REMARK 3 (A) PROTEIN: 131 SEQUENTIAL (|I-J|=1), 63 SHORT RANGE (1
REMARK 3 < |I-J| >=5), 67 LONG RANGE (|I-J|>5), AND 38 INTRARESIDUE
REMARK 3 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 120
REMARK 3 TORSION ANGLE RESTRAINTS (53 PHI, 13 PSI, 39 CHI1, 14
REMARK 3 CHI2, AND 1 CHI3), 39 THREE-BOND HN-HA COUPLING CONSTANT
REMARK 3 RESTRAINTS; NULL 75 (41 CALPHA AND 34 CBETA) 13C CHEMICAL
REMARK 3 SHIFT RESTRAINTS; NULL 49 RESIDUAL N-H DIPOLAR COUPLING
REMARK 3 RESTRAINTS; 20 DISTANCE RESTRAINTS FOR 10 BACKBONE
REMARK 3 HYDROGEN BONDS.
REMARK 3
REMARK 3 (B) DNA: 75 INTRARESIDUE, 124 SEQUENTIAL INTRASTRAND AND
REMARK 3 22 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 63
REMARK 3 DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 170
REMARK 3 TORSION ANGLE RESTRAINTS FOR THE DNA BACKBONE COVERING
REMARK 3 VALUES CHARACTERISTIC OF BOTH A AND B DNA.
REMARK 3
REMARK 3 (C) 58 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS
REMARK 3
REMARK 3 (D) 2 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES
REMARK 3
REMARK 3 (E) 8 'REPULSIVE' RESTRAINTS
REMARK 3
REMARK 3 (F) 4 DISTANCE RESTRAINTS FOR 2 INTERMOLECULAR H-BONDS
REMARK 3 BETWEEN ARG 24 AND BASE OF GUA5.
REMARK 3
REMARK 3 THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED
REMARK 3 MEAN STRUCTURE AND THE LAST NUMERIC COLUMN REPRESENTS THE
REMARK 3 RMS OF THE 34 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
REMARK 3 FOUND IN PDB ENTRY 8GAT ABOUT THE MEAN COORDINATE
REMARK 3 POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA
REMARK 3 STRUCTURES HAS NO MEANING.
REMARK 3
REMARK 3 THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL
REMARK 3 AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR:
REMARK 3 POINT 1 84.440-108.009-106.934
REMARK 3 POINT 2 85.210-106.770-106.473
REMARK 4
REMARK 4 6GAT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000179820.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.1
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : 360 MHZ; 600 MHZ; 500 MHZ; 750
REMARK 210 MHZ
REMARK 210 SPECTROMETER MODEL : AMX500; DMX500; AMX600; DMX600;
REMARK 210 DMX750; AM360
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR MODIFIED MODIFIED
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 34
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : REGULARIZED MEAN STRUCTURE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: DATA WERE RECORDED ON A 1:1 COMPLEX
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O MET A 1 H ASN A 3 1.18
REMARK 500 O ASN A 26 H GLY A 29 1.58
REMARK 500 O MET A 1 N ASN A 3 2.11
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 DT C 117 C5 DT C 117 C7 0.036
REMARK 500 DT C 121 C5 DT C 121 C7 0.037
REMARK 500
REMARK 500 REMARK: NULL
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 DA B 102 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DA B 102 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DG B 103 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DT B 104 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DG B 105 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DA B 106 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DA B 106 N1 - C2 - N3 ANGL. DEV. = -3.0 DEGREES
REMARK 500 DT B 107 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DA B 108 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DA B 108 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DG B 109 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DA B 110 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DA B 110 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DG B 111 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DA B 112 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DA B 112 N1 - C2 - N3 ANGL. DEV. = -3.0 DEGREES
REMARK 500 DC B 113 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG C 114 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DT C 115 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DC C 116 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DT C 117 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DC C 118 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DT C 119 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DA C 120 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DA C 120 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DT C 121 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DC C 122 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DA C 123 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DA C 123 N1 - C2 - N3 ANGL. DEV. = -3.0 DEGREES
REMARK 500 DC C 124 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DT C 125 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG C 126 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 LYS A 2 -38.12 49.97
REMARK 500 ASN A 3 136.57 66.19
REMARK 500 GLU A 5 -94.18 52.19
REMARK 500 ASN A 7 93.06 -14.51
REMARK 500 PRO A 9 110.91 -20.85
REMARK 500 THR A 10 95.34 -52.32
REMARK 500 PHE A 16 0.05 59.36
REMARK 500 PRO A 27 -1.23 -44.78
REMARK 500 VAL A 46 156.17 -48.79
REMARK 500 PRO A 48 96.35 -49.05
REMARK 500 LYS A 52 155.33 -43.93
REMARK 500 ASN A 60 -168.00 -73.38
REMARK 500 SER A 63 87.04 -55.08
REMARK 500 ALA A 64 -138.90 -61.31
REMARK 500 ASN A 65 -160.01 68.63
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 67 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 12 SG
REMARK 620 2 CYS A 15 SG 107.8
REMARK 620 3 CYS A 33 SG 109.5 111.2
REMARK 620 4 CYS A 36 SG 109.2 110.0 109.1
REMARK 620 N 1 2 3
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 67
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 7GAT RELATED DB: PDB
REMARK 900 ENSEMBLE OF 34 STRUCTURES
DBREF 6GAT A 1 66 UNP P17429 AREA_EMENI 662 727
DBREF 6GAT B 101 113 PDB 6GAT 6GAT 101 113
DBREF 6GAT C 114 126 PDB 6GAT 6GAT 114 126
SEQADV 6GAT MET A 1 UNP P17429 THR 662 CONFLICT
SEQADV 6GAT VAL A 22 UNP P17429 LEU 683 ENGINEERED MUTATION
SEQRES 1 B 13 DC DA DG DT DG DA DT DA DG DA DG DA DC
SEQRES 1 C 13 DG DT DC DT DC DT DA DT DC DA DC DT DG
SEQRES 1 A 66 MET LYS ASN GLY GLU GLN ASN GLY PRO THR THR CYS THR
SEQRES 2 A 66 ASN CYS PHE THR GLN THR THR PRO VAL TRP ARG ARG ASN
SEQRES 3 A 66 PRO GLU GLY GLN PRO LEU CYS ASN ALA CYS GLY LEU PHE
SEQRES 4 A 66 LEU LYS LEU HIS GLY VAL VAL ARG PRO LEU SER LEU LYS
SEQRES 5 A 66 THR ASP VAL ILE LYS LYS ARG ASN ARG ASN SER ALA ASN
SEQRES 6 A 66 SER
HET ZN A 67 1
HETNAM ZN ZINC ION
FORMUL 4 ZN ZN 2+
HELIX 1 1 ASN A 34 HIS A 43 1 10
HELIX 2 2 LEU A 49 LEU A 51 5 3
SHEET 1 A 2 ARG A 24 ARG A 25 0
SHEET 2 A 2 PRO A 31 LEU A 32 -1 O LEU A 32 N ARG A 24
LINK SG CYS A 12 ZN ZN A 67 1555 1555 2.27
LINK SG CYS A 15 ZN ZN A 67 1555 1555 2.30
LINK SG CYS A 33 ZN ZN A 67 1555 1555 2.31
LINK SG CYS A 36 ZN ZN A 67 1555 1555 2.28
SITE 1 AC1 4 CYS A 12 CYS A 15 CYS A 33 CYS A 36
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
Complete list - 3 20 Bytes