HEADER TRANSCRIPTION/DNA 07-NOV-97 6GAT TITLE SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING TITLE 2 DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA TITLE 3 SITE, REGULARIZED MEAN STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*AP*GP*TP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3'); COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*AP*CP*TP*G)-3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: NITROGEN REGULATORY PROTEIN AREA; COMPND 13 CHAIN: A; COMPND 14 FRAGMENT: DNA BINDING DOMAIN; COMPND 15 ENGINEERED: YES; COMPND 16 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 KEYWDS 2 DOMAIN, COMPLEX (TRANSCRIPTION REGULATION/DNA), KEYWDS 3 TRANSCRIPTION/DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,M.STARICH,M.WIKSTROM,A.M.GRONENBORN 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 JRNL TITL 2 AREA DNA BINDING DOMAIN COMPLEXED WITH A TGATAG JRNL TITL 3 CORE ELEMENT DEFINES A ROLE FOR HYDROPHOBIC JRNL TITL 4 PACKING IN THE DETERMINATION OF 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 1 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. 3.15, 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) : 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, REMARK 210 750 MHZ REMARK 210 SPECTROMETER MODEL : AMX500, DMX500, AMX600, REMARK 210 DMX600, 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 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 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 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 ZN ZN A 67 SG CYS A 12 1555 1555 2.27 LINK ZN ZN A 67 SG CYS A 15 1555 1555 2.30 LINK ZN ZN A 67 SG CYS A 33 1555 1555 2.31 LINK ZN ZN A 67 SG CYS A 36 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 MASTER 234 0 1 2 2 0 1 6 0 0 0 8 END