Header list of 1gat.pdb file
Complete list - 12 20 Bytes
HEADER TRANSCRIPTION/DNA 28-JUN-93 1GAT TITLE SOLUTION STRUCTURE OF THE SPECIFIC DNA COMPLEX OF THE ZINC TITLE 2 CONTAINING DNA BINDING DOMAIN OF THE ERYTHROID TITLE 3 TRANSCRIPTION FACTOR GATA-1 BY MULTIDIMENSIONAL NMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*GP*AP*TP*AP*AP*AP*C)3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*GP*TP*TP*TP*AP*TP*CP*T)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ERYTHROID TRANSCRIPTION FACTOR GATA-1; COMPND 11 CHAIN: A; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 3; SOURCE 7 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 8 ORGANISM_COMMON: CHICKEN; SOURCE 9 ORGANISM_TAXID: 9031; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA, NMR, DOUBLE HELIX, DNA/TRANSCRIPTION FACTOR COMPLEX, KEYWDS 2 TRANSCRIPTION/DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,J.G.OMICHINSKI,A.M.GRONENBORN REVDAT 2 24-FEB-09 1GAT 1 VERSN REVDAT 1 31-OCT-93 1GAT 0 JRNL AUTH J.G.OMICHINSKI,G.M.CLORE,M.ROBIEN,K.SAKAGUCHI, JRNL AUTH 2 E.APPELLA,A.M.GRONENBORN JRNL TITL HIGH-RESOLUTION SOLUTION STRUCTURE OF THE DOUBLE JRNL TITL 2 CYS2HIS2 ZINC FINGER FROM THE HUMAN ENHANCER JRNL TITL 3 BINDING PROTEIN MBP-1. JRNL REF BIOCHEMISTRY V. 31 3907 1992 JRNL REFN ISSN 0006-2960 JRNL PMID 1567844 JRNL DOI 10.1021/BI00131A004 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL REMARK 3 STATISTICS ARE GIVEN IN THE REFERENCE CITED ON THE *JRNL* REMARK 3 RECORDS ABOVE (I.E. AGREEMENT WITH EXPERIMENTAL RESTRAINTS, REMARK 3 DEVIATIONS FROM IDEALITY FOR BOND LENGTHS, ANGLES, PLANES REMARK 3 AND CHIRALITY, NON-BONDED CONTACTS, ATOMIC RMS DIFFERENCES REMARK 3 BETWEEN THE CALCULATED STRUCTURES). THE STRUCTURES ARE REMARK 3 BASED ON A TOTAL OF 1740 EXPERIMENTAL NMR RESTRAINTS REMARK 3 COMPRISING: 1444 INTERPROTON DISTANCE RESTRAINTS DERIVED REMARK 3 FROM NOE MEASUREMENTS; AND 296 TORSION ANGLE RESTRAINTS. REMARK 3 THE NOE RESTRAINTS ARE SUBDIVIDED AS FOLLOWS: (A) WITHIN REMARK 3 THE PROTEIN: 242 INTERRESIDUE SEQUENTIAL (|I-J|=1); 161 REMARK 3 INTERRESIDUE SHORT RANGE (1(LESS THAN)|I-J|(LESS THAN)=5); REMARK 3 182 INTERRESIDUE LONG RANGE (|I-J|(GREATER THAN)5); AND REMARK 3 334 INTRARESIDUE. (B) WITHIN THE DNA: 157 INTRARESIDUE; REMARK 3 180 SEQUENTIAL INTRASTRAND; 34 INTERSTRAND; AND 37 REMARK 3 H-BONDS (C) BETWEEN PROTEIN AND DNA: 117. THE TORSION REMARK 3 ANGLE RESTRAINTS ARE SUBDIVIDED AS FOLLOWS: 144 ANGLES REMARK 3 FOR THE PROTEIN (58 PHI, 56 PSI, 26 CHI1 AND 4 CHI2) AND REMARK 3 152 FOR THE DNA. THE TORSION ANGLE RESTRAINTS FOR THE REMARK 3 DNA COMPRISE LOOSE RESTRAINTS ON THE BACKBONE TORSION REMARK 3 ANGLES ALPHA, BETA, GAMMA, EPSILON AND ZETA TO PREVENT REMARK 3 PROBLEMS ASSOCIATED WITH LOCAL MIRROR IMAGES. REMARK 3 REMARK 3 THE METHOD USED TO DETERMINE THE STRUCTURES IS THE HYBRID REMARK 3 METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED REMARK 3 ANNEALING METHOD [M.NILGES, G.M.CLORE, AND A.M.GRONENBORN REMARK 3 FEBS LETT. 229, 317-324 (1988)]. REMARK 3 REMARK 3 A TOTAL OF 30 STRUCTURES WERE CALCULATED. THE ATOMIC RMS REMARK 3 DISTRIBUTION ABOUT THE MEAN COORDINATE POSITIONS FOR REMARK 3 RESIDUES 2 - 59 OF THE PROTEIN AND BASE PAIRS 6 - 13 OF THE REMARK 3 DNA IS 0.70 (+/-0.13) A FOR THE BACKBONE ATOMS OF THE REMARK 3 PROTEIN AND ALL ATOMS OF THE DNA, AND 1.13 (+/-0.08) A FOR REMARK 3 ALL ATOMS OF THE PROTEIN AND DNA. THE N-TERMINUS REMARK 3 (RESIDUE 1) AND C-TERMINUS (RESIDUES 60 - 66) ARE REMARK 3 DISORDERED. THE ORIENTATION OF THE FIRST 5 AND LAST 3 BASE REMARK 3 PAIRS OF THE 16MER DNA DUPLEX, WHICH ARE NOT IN CONTACT REMARK 3 WITH THE DNA, IS POORLY DEFINED WITH RESPECT TO THE CORE OF REMARK 3 THE COMPLEX. CONSEQUENTLY, ONLY THE COORDINATES OF THE REMARK 3 COMPLEX PROPER HAVE BEEN DEPOSITED: I.E. RESIDUES 1 - 60 REMARK 3 OF THE PROTEIN AND BASE PAIRS 6 - 13 OF THE DNA. REMARK 3 THE COORDINATES OF THE 30 INDIVIDUAL SA STRUCTURES ARE REMARK 3 PRESENTED AS MODELS 1 TO 30 IN PROTEIN DATA BANK ENTRY REMARK 3 1GAU. THE QUANTITY IN COLUMNS 61 - 66 OF THESE MODELS HAS REMARK 3 NO MEANING. REMARK 3 REMARK 3 THE COORDINATES OF THE RESTRAINED MINIMIZED STRUCTURE REMARK 3 ARE PRESENTED IN THIS ENTRY. THE (SA)R RESTRAINED REMARK 3 MINIMIZED MEAN STRUCTURE WAS DERIVED BY AVERAGING THE REMARK 3 COORDINATES OF THE INDIVIDUAL SA STRUCTURES (BEST FITTED TO REMARK 3 RESIDUES 2 - 59 OF THE PROTEIN AND BASE PAIRS 6 - 13 OF THE REMARK 3 DNA), AND SUBJECTING THE RESULTING COORDINATES TO REMARK 3 RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN COLUMNS REMARK 3 61 - 66 OF THE MEAN STRUCTURE, PRESENTED IN THIS ENTRY, REMARK 3 REPRESENTS THE ATOMIC RMS DEVIATIONS OF THE 30 INDIVIDUAL REMARK 3 SA STRUCTURES ABOUT THE MEAN STRUCTURE. REMARK 4 REMARK 4 1GAT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL 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 : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE COORDINATES OF THE RESTRAINED MINIMIZED STRUCTURE REMARK 210 ARE PRESENTED IN THIS ENTRY. THE (SA)R RESTRAINED MINIMIZED REMARK 210 MEAN STRUCTURE WAS DERIVED BY AVERAGING THE COORDINATES OF THE REMARK 210 INDIVIDUAL SA STRUCTURES (BEST FITTED TO RESIDUES 2 - 59 OF REMARK 210 THE PROTEIN AND BASE PAIRS 6 - 13 OF THE DNA), AND SUBJECTING REMARK 210 THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE REMARK 210 QUANTITY PRESENTED IN COLUMNS 61 - 66 OF THE MEAN STRUCTURE, REMARK 210 PRESENTED IN THIS ENTRY, REPRESENTS THE ATOMIC RMS DEVIATIONS REMARK 210 OF THE 30 INDIVIDUAL SA STRUCTURES ABOUT THE MEAN STRUCTURE. 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 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 106 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 106 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 106 N7 - C8 - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 DA B 106 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 107 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 107 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG B 107 N7 - C8 - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 DG B 107 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 108 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 108 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 108 N7 - C8 - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DA B 108 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 DT B 109 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 110 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 110 C5 - N7 - C8 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 110 N7 - C8 - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 DA B 110 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 111 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 111 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 111 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DA B 111 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA B 112 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA B 112 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 112 N7 - C8 - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 DA B 112 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 DC B 113 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG C 120 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG C 120 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG C 120 N7 - C8 - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG C 120 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT C 121 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT C 121 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT C 122 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT C 123 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 124 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA C 124 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA C 124 N7 - C8 - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 DA C 124 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT C 125 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC C 126 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT C 127 O4' - C1' - N1 ANGL. DEV. = 2.6 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 THR A 5 85.79 -67.81 REMARK 500 CYS A 10 17.21 -141.73 REMARK 500 GLN A 11 15.93 52.60 REMARK 500 LEU A 44 30.85 -74.62 REMARK 500 ASN A 55 96.86 -60.90 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 28 SG REMARK 620 2 CYS A 31 SG 108.5 REMARK 620 3 CYS A 7 SG 112.6 108.9 REMARK 620 4 CYS A 10 SG 110.2 109.8 106.8 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: 1GAU RELATED DB: PDB REMARK 900 ENSEMBLE OF 30 STRUCTURES DBREF 1GAT A 1 60 UNP P17678 GATA1_CHICK 158 217 DBREF 1GAT B 106 113 PDB 1GAT 1GAT 106 113 DBREF 1GAT C 120 127 PDB 1GAT 1GAT 120 127 SEQRES 1 B 8 DA DG DA DT DA DA DA DC SEQRES 1 C 8 DG DT DT DT DA DT DC DT SEQRES 1 A 60 LYS ARG ALA GLY THR VAL CYS SER ASN CYS GLN THR SER SEQRES 2 A 60 THR THR THR LEU TRP ARG ARG SER PRO MET GLY ASP PRO SEQRES 3 A 60 VAL CYS ASN ALA CYS GLY LEU TYR TYR LYS LEU HIS GLN SEQRES 4 A 60 VAL ASN ARG PRO LEU THR MET ARG LYS ASP GLY ILE GLN SEQRES 5 A 60 THR ARG ASN ARG LYS VAL SER SER HET ZN A 67 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ HELIX 1 1 ASN A 29 GLN A 39 1 11 HELIX 2 2 PRO A 43 ARG A 47 5 5 SHEET 1 A 2 TRP A 18 SER A 21 0 SHEET 2 A 2 ASP A 25 CYS A 28 -1 O ASP A 25 N SER A 21 LINK ZN ZN A 67 SG CYS A 28 1555 1555 2.32 LINK ZN ZN A 67 SG CYS A 31 1555 1555 2.29 LINK ZN ZN A 67 SG CYS A 7 1555 1555 2.28 LINK ZN ZN A 67 SG CYS A 10 1555 1555 2.28 SITE 1 AC1 4 CYS A 7 CYS A 10 CYS A 28 CYS A 31 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
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