PDB Short entry for 2R63 HEADER GENE REGULATING PROTEIN 13-NOV-96 2R63 TITLE STRUCTURAL ROLE OF A BURIED SALT BRIDGE IN THE 434 REPRESSOR DNA- TITLE 2 BINDING DOMAIN, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPRESSOR PROTEIN FROM BACTERIOPHAGE 434; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN, RESIDUES 1 - 63; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHAGE 434; SOURCE 3 ORGANISM_TAXID: 10712; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GENE REGULATING PROTEIN, PHAGE 434 REPRESSOR, HELIX-TURN-HELIX, DNA- KEYWDS 2 BINDING DOMAIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.V.PERVUSHIN,M.BILLETER,G.SIEGAL,K.WUTHRICH REVDAT 3 03-NOV-21 2R63 1 REMARK SEQADV REVDAT 2 24-FEB-09 2R63 1 VERSN REVDAT 1 16-JUN-97 2R63 0 JRNL AUTH K.PERVUSHIN,M.BILLETER,G.SIEGAL,K.WUTHRICH JRNL TITL STRUCTURAL ROLE OF A BURIED SALT BRIDGE IN THE 434 REPRESSOR JRNL TITL 2 DNA-BINDING DOMAIN. JRNL REF J.MOL.BIOL. V. 264 1002 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 9000626 JRNL DOI 10.1006/JMBI.1996.0692 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.NERI,M.BILLETER,K.WUTHRICH REMARK 1 TITL DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE SOLUTION REMARK 1 TITL 2 STRUCTURE OF THE DNA-BINDING DOMAIN (RESIDUES 1 TO 69) OF REMARK 1 TITL 3 THE 434 REPRESSOR AND COMPARISON WITH THE X-RAY CRYSTAL REMARK 1 TITL 4 STRUCTURE REMARK 1 REF J.MOL.BIOL. V. 223 743 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.MONDRAGON,S.SUBBIAH,S.C.ALMO,M.DROTTAR,S.C.HARRISON REMARK 1 TITL STRUCTURE OF THE AMINO-TERMINAL DOMAIN OF PHAGE 434 REMARK 1 TITL 2 REPRESSOR AT 2.0 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 205 189 1989 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPAL REMARK 3 AUTHORS : LUGINBUHL,GUNTERT,BILLETER,WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2R63 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178544. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 286 REMARK 210 PH : 4.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; E.COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITY PLUS 750 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VARIAN VNMR VNMR, DIANA, OPAL REMARK 210 METHOD USED : DISTANCE GEOMETRY WITH DIANA, REMARK 210 ENERGY MINIMIZATION WITH OPAL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : DIANA PENALTY FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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: 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 9 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 11 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 13 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -3.1 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 1 ARG A 43 33.81 -80.39 REMARK 500 1 PHE A 44 24.24 -167.36 REMARK 500 1 ASN A 61 -83.21 -83.71 REMARK 500 2 LYS A 40 -82.75 -85.89 REMARK 500 2 PHE A 44 39.22 -73.58 REMARK 500 2 LEU A 60 -72.99 -71.12 REMARK 500 2 ASN A 61 51.49 -156.72 REMARK 500 4 LYS A 38 -80.47 -105.29 REMARK 500 4 THR A 39 117.79 55.77 REMARK 500 4 PHE A 44 48.76 -75.87 REMARK 500 4 ASN A 61 -71.59 -137.46 REMARK 500 5 PHE A 44 35.21 -77.33 REMARK 500 5 ASN A 61 -80.38 -156.15 REMARK 500 6 LYS A 40 -69.74 -91.12 REMARK 500 6 PHE A 44 42.75 -80.77 REMARK 500 6 ASN A 61 -71.80 -100.74 REMARK 500 7 VAL A 6 -71.48 -65.18 REMARK 500 7 ASN A 36 7.83 -69.50 REMARK 500 7 LYS A 38 -62.89 -92.79 REMARK 500 7 LYS A 40 -79.48 -80.02 REMARK 500 7 ARG A 43 47.42 -79.05 REMARK 500 7 PHE A 44 19.32 -177.87 REMARK 500 7 LEU A 60 -73.09 -52.36 REMARK 500 7 ASN A 61 65.96 -156.87 REMARK 500 8 ASN A 36 0.31 -65.02 REMARK 500 8 LYS A 40 -63.72 -107.43 REMARK 500 8 PHE A 44 44.36 -80.36 REMARK 500 8 ASN A 61 -93.70 -130.96 REMARK 500 9 PRO A 42 -176.59 -66.44 REMARK 500 9 ASN A 61 13.23 -155.54 REMARK 500 10 LYS A 38 36.75 -90.55 REMARK 500 10 THR A 39 179.63 67.36 REMARK 500 10 PHE A 44 47.02 -80.02 REMARK 500 10 ASN A 61 -78.73 -96.33 REMARK 500 11 PHE A 44 40.20 -76.08 REMARK 500 11 ASN A 61 16.61 -152.18 REMARK 500 12 LYS A 40 -74.81 -66.51 REMARK 500 12 ARG A 43 34.46 -89.80 REMARK 500 12 PHE A 44 30.28 -154.10 REMARK 500 12 ASN A 61 -76.53 -99.22 REMARK 500 13 LYS A 9 -70.89 -60.84 REMARK 500 13 LYS A 38 35.86 -76.39 REMARK 500 13 THR A 39 164.41 72.80 REMARK 500 13 PHE A 44 36.62 -72.79 REMARK 500 13 ASN A 61 15.69 -156.76 REMARK 500 14 LYS A 40 -68.54 -108.61 REMARK 500 14 PHE A 44 44.74 -79.15 REMARK 500 15 ILE A 2 -53.85 -159.44 REMARK 500 15 ARG A 43 48.66 -77.90 REMARK 500 15 PHE A 44 25.69 -170.51 REMARK 500 REMARK 500 THIS ENTRY HAS 67 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 5 ARG A 43 0.11 SIDE CHAIN REMARK 500 8 ARG A 41 0.09 SIDE CHAIN REMARK 500 8 ARG A 43 0.07 SIDE CHAIN REMARK 500 9 ARG A 5 0.15 SIDE CHAIN REMARK 500 10 ARG A 5 0.10 SIDE CHAIN REMARK 500 10 ARG A 43 0.10 SIDE CHAIN REMARK 500 14 ARG A 5 0.10 SIDE CHAIN REMARK 500 14 ARG A 41 0.14 SIDE CHAIN REMARK 500 14 ARG A 43 0.11 SIDE CHAIN REMARK 500 15 ARG A 5 0.09 SIDE CHAIN REMARK 500 16 ARG A 41 0.10 SIDE CHAIN REMARK 500 17 ARG A 5 0.11 SIDE CHAIN REMARK 500 17 ARG A 41 0.09 SIDE CHAIN REMARK 500 19 ARG A 41 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2R63 A 1 63 UNP P16117 RPC1_BP434 1 63 SEQADV 2R63 MET A 10 UNP P16117 ARG 10 ENGINEERED MUTATION SEQRES 1 A 63 SER ILE SER SER ARG VAL LYS SER LYS MET ILE GLN LEU SEQRES 2 A 63 GLY LEU ASN GLN ALA GLU LEU ALA GLN LYS VAL GLY THR SEQRES 3 A 63 THR GLN GLN SER ILE GLU GLN LEU GLU ASN GLY LYS THR SEQRES 4 A 63 LYS ARG PRO ARG PHE LEU PRO GLU LEU ALA SER ALA LEU SEQRES 5 A 63 GLY VAL SER VAL ASP TRP LEU LEU ASN GLY THR HELIX 1 H1 ILE A 2 LEU A 13 5 12 HELIX 2 H2 GLN A 17 VAL A 24 5 8 HELIX 3 H3 GLN A 28 GLU A 35 5 8 HELIX 4 H4 LEU A 45 LEU A 52 5 8 HELIX 5 H5 VAL A 56 ASN A 61 5 6 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