HEADER ISOMERASE 07-FEB-02 1KZN TITLE CRYSTAL STRUCTURE OF E. COLI 24KDA DOMAIN IN COMPLEX WITH CLOROBIOCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 24 KDA N-TERMINUS DOMAIN; COMPND 5 SYNONYM: GYRASE B; COMPND 6 EC: 5.99.1.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOPOISOMERASE, GYRASE B, CLOROBIOCIN, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.LAFITTE,V.LAMOUR,P.O.TSVETKOV,A.A.MAKAROV,M.KLICH,P.DEPREZ,D.MORAS, AUTHOR 2 C.BRIAND,R.GILLI REVDAT 3 14-FEB-24 1KZN 1 REMARK REVDAT 2 24-FEB-09 1KZN 1 VERSN REVDAT 1 19-JUN-02 1KZN 0 JRNL AUTH D.LAFITTE,V.LAMOUR,P.O.TSVETKOV,A.A.MAKAROV,M.KLICH, JRNL AUTH 2 P.DEPREZ,D.MORAS,C.BRIAND,R.GILLI JRNL TITL DNA GYRASE INTERACTION WITH COUMARIN-BASED INHIBITORS: THE JRNL TITL 2 ROLE OF THE HYDROXYBENZOATE ISOPENTENYL MOIETY AND THE JRNL TITL 3 5'-METHYL GROUP OF THE NOVIOSE. JRNL REF BIOCHEMISTRY V. 41 7217 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12044152 JRNL DOI 10.1021/BI0159837 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1321043.850 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 9166 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM 5% REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 454 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1394 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 72 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.45000 REMARK 3 B22 (A**2) : -0.67000 REMARK 3 B33 (A**2) : -1.78000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.780 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.780 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.590 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.48 REMARK 3 BSOL : 110.2 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CLO.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CLO.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-96 REMARK 200 TEMPERATURE (KELVIN) : 140 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.938 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16938 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20000,PROPANOL-2,HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 20.35700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.79950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.81450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.79950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.35700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.81450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A 82A REMARK 465 PRO A 82B REMARK 465 GLU A 82C REMARK 465 GLU A 82D REMARK 465 GLY A 101 REMARK 465 GLY A 102 REMARK 465 LYS A 103 REMARK 465 PHE A 104 REMARK 465 ASP A 105 REMARK 465 ASP A 106 REMARK 465 ASN A 107 REMARK 465 SER A 108 REMARK 465 TYR A 109 REMARK 465 LYS A 110 REMARK 465 VAL A 111 REMARK 465 SER A 112 REMARK 465 GLY A 113 REMARK 465 GLY A 114 REMARK 465 LEU A 115 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NE2 GLN A 151 O HOH A 1031 0.79 REMARK 500 CD GLN A 151 O HOH A 1031 0.92 REMARK 500 OE1 GLN A 151 O HOH A 1031 1.46 REMARK 500 OE2 GLU A 88 O HOH A 1033 2.15 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 LEU A 16 -82.50 -6.67 REMARK 500 HIS A 95 42.33 37.29 REMARK 500 ASN A 178 -86.53 63.12 REMARK 500 ASP A 210 8.80 -150.52 REMARK 500 HIS A 217 58.96 -164.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CBN A 1 DBREF 1KZN A 15 219 UNP P06982 GYRB_ECOLI 14 218 SEQRES 1 A 205 GLY LEU ASP ALA VAL ARG LYS ARG PRO GLY MET TYR ILE SEQRES 2 A 205 GLY ASP THR ASP ASP GLY THR GLY LEU HIS HIS MET VAL SEQRES 3 A 205 PHE GLU VAL VAL ASP ASN ALA ILE ASP GLU ALA LEU ALA SEQRES 4 A 205 GLY HIS CYS LYS GLU ILE ILE VAL THR ILE HIS ALA ASP SEQRES 5 A 205 ASN SER VAL SER VAL GLN ASP ASP GLY ARG GLY ILE PRO SEQRES 6 A 205 THR GLY ILE HIS PRO GLU GLU GLY VAL SER ALA ALA GLU SEQRES 7 A 205 VAL ILE MET THR VAL LEU HIS ALA GLY GLY LYS PHE ASP SEQRES 8 A 205 ASP ASN SER TYR LYS VAL SER GLY GLY LEU HIS GLY VAL SEQRES 9 A 205 GLY VAL SER VAL VAL ASN ALA LEU SER GLN LYS LEU GLU SEQRES 10 A 205 LEU VAL ILE GLN ARG GLU GLY LYS ILE HIS ARG GLN ILE SEQRES 11 A 205 TYR GLU HIS GLY VAL PRO GLN ALA PRO LEU ALA VAL THR SEQRES 12 A 205 GLY GLU THR GLU LYS THR GLY THR MET VAL ARG PHE TRP SEQRES 13 A 205 PRO SER LEU GLU THR PHE THR ASN VAL THR GLU PHE GLU SEQRES 14 A 205 TYR GLU ILE LEU ALA LYS ARG LEU ARG GLU LEU SER PHE SEQRES 15 A 205 LEU ASN SER GLY VAL SER ILE ARG LEU ARG ASP LYS ARG SEQRES 16 A 205 ASP GLY LYS GLU ASP HIS PHE HIS TYR GLU HET CBN A 1 49 HETNAM CBN CLOROBIOCIN FORMUL 2 CBN C35 H37 CL N2 O11 FORMUL 3 HOH *164(H2 O) HELIX 1 1 GLY A 15 ARG A 22 1 8 HELIX 2 2 ARG A 22 GLY A 28 1 7 HELIX 3 3 GLY A 33 ALA A 53 1 21 HELIX 4 4 SER A 85 VAL A 93 1 9 HELIX 5 5 GLY A 119 LEU A 126 1 8 HELIX 6 6 GLU A 183 ASN A 198 1 16 SHEET 1 A 8 GLU A 213 PHE A 216 0 SHEET 2 A 8 SER A 202 ASP A 207 -1 N ILE A 203 O PHE A 216 SHEET 3 A 8 GLU A 58 HIS A 64 1 N VAL A 61 O ARG A 204 SHEET 4 A 8 SER A 68 ASP A 73 -1 O GLN A 72 N ILE A 60 SHEET 5 A 8 GLY A 164 PRO A 171 -1 O VAL A 167 N VAL A 71 SHEET 6 A 8 SER A 127 ARG A 136 -1 N GLU A 131 O ARG A 168 SHEET 7 A 8 LYS A 139 GLU A 146 -1 O GLN A 143 N LEU A 132 SHEET 8 A 8 VAL A 149 PRO A 150 -1 O VAL A 149 N GLU A 146 SHEET 1 B 8 GLU A 213 PHE A 216 0 SHEET 2 B 8 SER A 202 ASP A 207 -1 N ILE A 203 O PHE A 216 SHEET 3 B 8 GLU A 58 HIS A 64 1 N VAL A 61 O ARG A 204 SHEET 4 B 8 SER A 68 ASP A 73 -1 O GLN A 72 N ILE A 60 SHEET 5 B 8 GLY A 164 PRO A 171 -1 O VAL A 167 N VAL A 71 SHEET 6 B 8 SER A 127 ARG A 136 -1 N GLU A 131 O ARG A 168 SHEET 7 B 8 LYS A 139 GLU A 146 -1 O GLN A 143 N LEU A 132 SHEET 8 B 8 ALA A 155 GLU A 159 -1 O ALA A 155 N ARG A 142 SITE 1 AC1 19 ARG A 22 TYR A 26 ASN A 46 GLU A 50 SITE 2 AC1 19 VAL A 71 ASP A 73 ARG A 76 GLY A 77 SITE 3 AC1 19 ILE A 78 PRO A 79 ILE A 90 HIS A 95 SITE 4 AC1 19 ARG A 136 THR A 165 HOH A1122 HOH A1154 SITE 5 AC1 19 HOH A1160 HOH A1172 HOH A1176 CRYST1 40.714 47.629 111.599 90.00 90.00 90.00 P 21 21 21 4 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 0.024562 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008961 0.00000