PDB Short entry for 4GAT HEADER TRANSCRIPTION/DNA 07-NOV-97 4GAT TITLE SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA TITLE 2 COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN TITLE 3 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*GP*CP*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*GP*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 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 ORGAN: TAIL; SOURCE 9 GENE: POTENTIAL; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 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 16-MAR-22 4GAT 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 4GAT 1 VERSN REVDAT 2 01-APR-03 4GAT 1 JRNL REVDAT 1 28-JAN-98 4GAT 0 JRNL AUTH M.R.STARICH,M.WIKSTROM,H.N.ARST JR.,G.M.CLORE,A.M.GRONENBORN JRNL TITL THE SOLUTION STRUCTURE OF A FUNGAL AREA PROTEIN-DNA COMPLEX: JRNL TITL 2 AN ALTERNATIVE BINDING MODE FOR THE BASIC CARBOXYL TAIL OF JRNL TITL 3 GATA FACTORS. JRNL REF J.MOL.BIOL. V. 277 605 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9533883 JRNL DOI 10.1006/JMBI.1998.1625 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 WILD TYPE 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 1098 EXPERIMENTAL RESTRAINTS REMARK 3 REMARK 3 (A) PROTEIN: 119 SEQUENTIAL (|I-J|=1), 49 SHORT RANGE (1 REMARK 3 < |I-J| >=5), 68 LONG RANGE (|I-J|>5), AND 64 INTRARESIDUE REMARK 3 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 124 REMARK 3 TORSION ANGLE RESTRAINTS (61 PHI, 8 PSI, 39 CHI1, 15 CHI2, REMARK 3 AND 1 CHI3), 41 THREE-BOND HN-HA COUPLING CONSTANT REMARK 3 RESTRAINTS; NULL 77 (41 CALPHA AND 36 CBETA) 13C CHEMICAL REMARK 3 SHIFT RESTRAINTS; NULL 48 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, 115 SEQUENTIAL INTRASTRAND AND REMARK 3 20 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 66 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) 48 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 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES REMARK 3 FOUND IN PDB ENTRY 5GAT 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 1 115.014-147.742 -73.887 REMARK 3 POINT 2 115.768-146.457 -73.538 REMARK 4 REMARK 4 4GAT 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_1000179324. 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; AND 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 : 35 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 H ASN A 3 H GLY A 4 1.09 REMARK 500 HD21 ASN A 7 H GLY A 8 1.21 REMARK 500 H ASN A 26 O GLN A 30 1.49 REMARK 500 O ARG A 24 H LEU A 32 1.58 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 115 C5 DT C 115 C7 0.037 REMARK 500 DT C 119 C5 DT C 119 C7 0.036 REMARK 500 DT C 121 C5 DT C 121 C7 0.039 REMARK 500 DT C 125 C5 DT C 125 C7 0.036 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 DC B 101 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA B 102 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 102 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 103 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 104 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 105 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 106 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 106 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT B 107 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 108 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 108 N1 - C2 - N3 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG B 109 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 110 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 111 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 112 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 112 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC B 113 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG C 114 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT C 115 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC C 116 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT C 117 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC C 118 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT C 119 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 120 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 121 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG C 123 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC C 124 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT C 125 O4' - C1' - N1 ANGL. DEV. = 2.1 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 99.70 -66.58 REMARK 500 ASN A 3 -15.73 -161.55 REMARK 500 GLU A 5 75.13 -152.96 REMARK 500 ASN A 7 -41.42 -139.09 REMARK 500 PHE A 16 7.56 57.82 REMARK 500 PRO A 27 -11.93 -44.30 REMARK 500 CYS A 33 -145.46 -85.73 REMARK 500 VAL A 46 161.58 -49.00 REMARK 500 PRO A 48 98.37 -47.83 REMARK 500 LEU A 49 -7.06 -57.03 REMARK 500 ASN A 60 -155.51 -74.88 REMARK 500 ASN A 62 24.98 -72.59 REMARK 500 ALA A 64 -90.78 179.62 REMARK 500 ASN A 65 -72.18 -179.99 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 108.1 REMARK 620 3 CYS A 33 SG 109.9 110.4 REMARK 620 4 CYS A 36 SG 109.6 110.8 108.1 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: 5GAT RELATED DB: PDB REMARK 900 ENSEMBLE OF 35 STRUCTURES DBREF 4GAT A 1 66 UNP P17429 AREA_EMENI 662 727 DBREF 4GAT B 101 113 PDB 4GAT 4GAT 101 113 DBREF 4GAT C 114 126 PDB 4GAT 4GAT 114 126 SEQADV 4GAT MET A 1 UNP P17429 THR 662 CONFLICT SEQRES 1 B 13 DC DA DG DC DG DA DT DA DG DA DG DA DC SEQRES 1 C 13 DG DT DC DT DC DT DA DT DC DG 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 LEU 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 ALA A 35 HIS A 43 1 9 HELIX 2 2 LEU A 49 LEU A 51 5 3 SHEET 1 A 2 ARG A 24 ASN A 26 0 SHEET 2 A 2 GLN A 30 LEU A 32 -1 N LEU A 32 O ARG A 24 LINK SG CYS A 12 ZN ZN A 67 1555 1555 2.29 LINK SG CYS A 15 ZN ZN A 67 1555 1555 2.30 LINK SG CYS A 33 ZN ZN A 67 1555 1555 2.30 LINK SG CYS A 36 ZN ZN A 67 1555 1555 2.29 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