HEADER ISOMERASE 02-FEB-18 5Z9E TITLE BACTERIAL GYRB ATPASE DOMAIN IN COMPLEX WITH A CHEMICAL FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE SUBUNIT B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 15-221; COMPND 5 SYNONYM: TYPE IIA TOPOISOMERASE SUBUNIT GYRB; COMPND 6 EC: 5.99.1.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: GYRB, ACRB, COU, HIMB, HISU, NALC, PARA, PCBA, B3699, JW5625; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA TOPOISOMERASE, ANTIBACTERIAL, DRUG TARGET, FRAGMENT-BASE LEAD KEYWDS 2 DISCOVERY, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR X.HUANG,H.ZHOU REVDAT 2 22-NOV-23 5Z9E 1 REMARK REVDAT 1 12-DEC-18 5Z9E 0 JRNL AUTH X.HUANG,J.GUO,Q.LIU,Q.GU,J.XU,H.ZHOU JRNL TITL IDENTIFICATION OF AN AUXILIARY DRUGGABLE POCKET IN THE DNA JRNL TITL 2 GYRASE ATPASE DOMAIN USING FRAGMENT PROBES JRNL REF MEDCHEMCOMM V. 9 1619 2018 JRNL REFN ESSN 2040-2511 JRNL PMID 30429968 JRNL DOI 10.1039/C8MD00148K REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 37995 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 REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1922 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2755 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.2330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2856 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.76000 REMARK 3 B22 (A**2) : 1.20000 REMARK 3 B33 (A**2) : -0.44000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.123 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.902 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2974 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2816 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4028 ; 1.307 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6451 ; 0.934 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 370 ; 5.260 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;39.771 ;23.824 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 487 ;11.159 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ; 9.728 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 455 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3504 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 678 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1489 ; 0.921 ; 1.996 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1488 ; 0.922 ; 1.996 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1856 ; 1.575 ; 2.985 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1857 ; 1.574 ; 2.986 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1485 ; 1.207 ; 2.228 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1486 ; 1.206 ; 2.228 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2173 ; 2.007 ; 3.265 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3172 ; 3.742 ;16.196 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3173 ; 3.742 ;16.198 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 16 A 218 REMARK 3 ORIGIN FOR THE GROUP (A): 27.4691 16.4983 16.7296 REMARK 3 T TENSOR REMARK 3 T11: 0.0259 T22: 0.0082 REMARK 3 T33: 0.0092 T12: -0.0136 REMARK 3 T13: 0.0100 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.9465 L22: 1.0242 REMARK 3 L33: 0.7919 L12: 0.5536 REMARK 3 L13: -0.1875 L23: -0.4418 REMARK 3 S TENSOR REMARK 3 S11: -0.0225 S12: 0.0248 S13: -0.0792 REMARK 3 S21: 0.0018 S22: 0.0209 S23: -0.0442 REMARK 3 S31: -0.0497 S32: 0.0339 S33: 0.0016 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 16 B 220 REMARK 3 ORIGIN FOR THE GROUP (A): 1.4133 -10.5876 9.1287 REMARK 3 T TENSOR REMARK 3 T11: 0.0091 T22: 0.0244 REMARK 3 T33: 0.0550 T12: -0.0043 REMARK 3 T13: -0.0068 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.8884 L22: 0.4832 REMARK 3 L33: 0.7171 L12: 0.2395 REMARK 3 L13: -0.6208 L23: 0.0812 REMARK 3 S TENSOR REMARK 3 S11: -0.0082 S12: 0.0438 S13: -0.1184 REMARK 3 S21: 0.0004 S22: -0.0135 S23: -0.0554 REMARK 3 S31: -0.0078 S32: -0.0346 S33: 0.0217 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5Z9E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39968 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 57.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4DUH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 7.5, 2.20M REMARK 280 (NH4)2HPO4, 10MM 2-AMINOBENZIMIDAZOLE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 285K 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 30.68950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.35050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.27900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.35050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.68950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.27900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A 15 REMARK 465 HIS A 99 REMARK 465 ALA A 100 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 465 HIS A 116 REMARK 465 GLU A 219 REMARK 465 GLY A 220 REMARK 465 GLY A 221 REMARK 465 GLY B 15 REMARK 465 HIS B 99 REMARK 465 ALA B 100 REMARK 465 GLY B 101 REMARK 465 GLY B 102 REMARK 465 LYS B 103 REMARK 465 PHE B 104 REMARK 465 ASP B 105 REMARK 465 ASP B 106 REMARK 465 ASN B 107 REMARK 465 SER B 108 REMARK 465 TYR B 109 REMARK 465 LYS B 110 REMARK 465 VAL B 111 REMARK 465 SER B 112 REMARK 465 GLY B 113 REMARK 465 GLY B 114 REMARK 465 LEU B 115 REMARK 465 HIS B 116 REMARK 465 GLY B 221 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 55 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 85 CG CD OE1 OE2 REMARK 470 LYS A 139 CE NZ REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 ARG B 22 CG CD NE CZ NH1 NH2 REMARK 470 MET B 25 CG SD CE REMARK 470 LYS B 57 NZ REMARK 470 GLU B 85 CG CD OE1 OE2 REMARK 470 GLU B 185 CG CD OE1 OE2 REMARK 470 LYS B 212 CG CD CE NZ REMARK 470 GLU B 219 CG CD OE1 OE2 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 57 60.04 61.10 REMARK 500 ASN A 178 -78.91 67.60 REMARK 500 ASN A 198 67.25 -107.96 REMARK 500 LYS B 57 83.87 55.65 REMARK 500 ASN B 178 -71.47 71.88 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 PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 27K A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 27K B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AX7 B 303 DBREF 5Z9E A 15 221 UNP P0AES6 GYRB_ECOLI 15 221 DBREF 5Z9E B 15 221 UNP P0AES6 GYRB_ECOLI 15 221 SEQRES 1 A 207 GLY LEU ASP ALA VAL ARG LYS ARG PRO GLY MET TYR ILE SEQRES 2 A 207 GLY ASP THR ASP ASP GLY THR GLY LEU HIS HIS MET VAL SEQRES 3 A 207 PHE GLU VAL VAL ASP ASN ALA ILE ASP GLU ALA LEU ALA SEQRES 4 A 207 GLY HIS CYS LYS GLU ILE ILE VAL THR ILE HIS ALA ASP SEQRES 5 A 207 ASN SER VAL SER VAL GLN ASP ASP GLY ARG GLY ILE PRO SEQRES 6 A 207 THR GLY ILE HIS PRO GLU GLU GLY VAL SER ALA ALA GLU SEQRES 7 A 207 VAL ILE MET THR VAL LEU HIS ALA GLY GLY LYS PHE ASP SEQRES 8 A 207 ASP ASN SER TYR LYS VAL SER GLY GLY LEU HIS GLY VAL SEQRES 9 A 207 GLY VAL SER VAL VAL ASN ALA LEU SER GLN LYS LEU GLU SEQRES 10 A 207 LEU VAL ILE GLN ARG GLU GLY LYS ILE HIS ARG GLN ILE SEQRES 11 A 207 TYR GLU HIS GLY VAL PRO GLN ALA PRO LEU ALA VAL THR SEQRES 12 A 207 GLY GLU THR GLU LYS THR GLY THR MET VAL ARG PHE TRP SEQRES 13 A 207 PRO SER LEU GLU THR PHE THR ASN VAL THR GLU PHE GLU SEQRES 14 A 207 TYR GLU ILE LEU ALA LYS ARG LEU ARG GLU LEU SER PHE SEQRES 15 A 207 LEU ASN SER GLY VAL SER ILE ARG LEU ARG ASP LYS ARG SEQRES 16 A 207 ASP GLY LYS GLU ASP HIS PHE HIS TYR GLU GLY GLY SEQRES 1 B 207 GLY LEU ASP ALA VAL ARG LYS ARG PRO GLY MET TYR ILE SEQRES 2 B 207 GLY ASP THR ASP ASP GLY THR GLY LEU HIS HIS MET VAL SEQRES 3 B 207 PHE GLU VAL VAL ASP ASN ALA ILE ASP GLU ALA LEU ALA SEQRES 4 B 207 GLY HIS CYS LYS GLU ILE ILE VAL THR ILE HIS ALA ASP SEQRES 5 B 207 ASN SER VAL SER VAL GLN ASP ASP GLY ARG GLY ILE PRO SEQRES 6 B 207 THR GLY ILE HIS PRO GLU GLU GLY VAL SER ALA ALA GLU SEQRES 7 B 207 VAL ILE MET THR VAL LEU HIS ALA GLY GLY LYS PHE ASP SEQRES 8 B 207 ASP ASN SER TYR LYS VAL SER GLY GLY LEU HIS GLY VAL SEQRES 9 B 207 GLY VAL SER VAL VAL ASN ALA LEU SER GLN LYS LEU GLU SEQRES 10 B 207 LEU VAL ILE GLN ARG GLU GLY LYS ILE HIS ARG GLN ILE SEQRES 11 B 207 TYR GLU HIS GLY VAL PRO GLN ALA PRO LEU ALA VAL THR SEQRES 12 B 207 GLY GLU THR GLU LYS THR GLY THR MET VAL ARG PHE TRP SEQRES 13 B 207 PRO SER LEU GLU THR PHE THR ASN VAL THR GLU PHE GLU SEQRES 14 B 207 TYR GLU ILE LEU ALA LYS ARG LEU ARG GLU LEU SER PHE SEQRES 15 B 207 LEU ASN SER GLY VAL SER ILE ARG LEU ARG ASP LYS ARG SEQRES 16 B 207 ASP GLY LYS GLU ASP HIS PHE HIS TYR GLU GLY GLY HET PO4 A 301 5 HET PO4 A 302 5 HET PO4 A 303 5 HET 27K A 304 14 HET PO4 B 301 5 HET 27K B 302 14 HET AX7 B 303 10 HETNAM PO4 PHOSPHATE ION HETNAM 27K BUTYL 4-HYDROXYBENZOATE HETNAM AX7 1H-BENZIMIDAZOL-2-AMINE FORMUL 3 PO4 4(O4 P 3-) FORMUL 6 27K 2(C11 H14 O3) FORMUL 9 AX7 C7 H7 N3 FORMUL 10 HOH *129(H2 O) HELIX 1 AA1 LEU A 16 ARG A 22 1 7 HELIX 2 AA2 ARG A 22 GLY A 28 1 7 HELIX 3 AA3 GLY A 33 ALA A 53 1 21 HELIX 4 AA4 SER A 89 VAL A 97 1 9 HELIX 5 AA5 GLY A 119 LEU A 126 1 8 HELIX 6 AA6 GLU A 183 ASN A 198 1 16 HELIX 7 AA7 ASP B 17 ARG B 22 1 6 HELIX 8 AA8 ARG B 22 GLY B 28 1 7 HELIX 9 AA9 GLY B 33 ALA B 53 1 21 HELIX 10 AB1 SER B 89 VAL B 97 1 9 HELIX 11 AB2 GLY B 119 LEU B 126 1 8 HELIX 12 AB3 GLU B 183 ASN B 198 1 16 SHEET 1 AA1 3 VAL A 149 PRO A 150 0 SHEET 2 AA1 3 LYS A 139 GLU A 146 -1 N GLU A 146 O VAL A 149 SHEET 3 AA1 3 ALA A 155 GLU A 159 -1 O ALA A 155 N ARG A 142 SHEET 1 AA2 8 VAL A 149 PRO A 150 0 SHEET 2 AA2 8 LYS A 139 GLU A 146 -1 N GLU A 146 O VAL A 149 SHEET 3 AA2 8 SER A 127 ARG A 136 -1 N LEU A 130 O TYR A 145 SHEET 4 AA2 8 GLY A 164 PRO A 171 -1 O ARG A 168 N GLU A 131 SHEET 5 AA2 8 VAL A 69 ASP A 73 -1 N ASP A 73 O THR A 165 SHEET 6 AA2 8 GLU A 58 ILE A 63 -1 N THR A 62 O SER A 70 SHEET 7 AA2 8 SER A 202 ASP A 207 1 O ARG A 206 N ILE A 63 SHEET 8 AA2 8 GLU A 213 PHE A 216 -1 O PHE A 216 N ILE A 203 SHEET 1 AA3 3 VAL B 149 PRO B 150 0 SHEET 2 AA3 3 LYS B 139 GLU B 146 -1 N GLU B 146 O VAL B 149 SHEET 3 AA3 3 ALA B 155 GLU B 159 -1 O GLY B 158 N ILE B 140 SHEET 1 AA4 8 VAL B 149 PRO B 150 0 SHEET 2 AA4 8 LYS B 139 GLU B 146 -1 N GLU B 146 O VAL B 149 SHEET 3 AA4 8 SER B 127 ARG B 136 -1 N ILE B 134 O HIS B 141 SHEET 4 AA4 8 GLY B 164 PRO B 171 -1 O GLY B 164 N GLN B 135 SHEET 5 AA4 8 VAL B 69 ASP B 73 -1 N VAL B 71 O VAL B 167 SHEET 6 AA4 8 GLU B 58 ILE B 63 -1 N THR B 62 O SER B 70 SHEET 7 AA4 8 SER B 202 ASP B 207 1 O ARG B 204 N VAL B 61 SHEET 8 AA4 8 GLU B 213 HIS B 217 -1 O PHE B 216 N ILE B 203 SITE 1 AC1 5 ARG A 20 LYS A 21 PRO A 23 HOH A 420 SITE 2 AC1 5 GLN B 151 SITE 1 AC2 5 HIS A 64 ARG A 168 LYS A 208 HOH A 429 SITE 2 AC2 5 HOH A 442 SITE 1 AC3 5 PRO A 150 GLN A 151 ARG B 20 LYS B 21 SITE 2 AC3 5 PRO B 23 SITE 1 AC4 9 VAL A 43 ASN A 46 GLU A 50 ILE A 78 SITE 2 AC4 9 PRO A 79 ILE A 94 VAL A 120 VAL A 167 SITE 3 AC4 9 HOH A 401 SITE 1 AC5 5 HIS B 55 HIS B 64 ARG B 168 LYS B 208 SITE 2 AC5 5 HOH B 406 SITE 1 AC6 7 VAL B 43 ASN B 46 GLU B 50 ILE B 78 SITE 2 AC6 7 ILE B 94 VAL B 167 HOH B 401 SITE 1 AC7 4 HIS A 147 GLU A 174 HIS B 147 GLU B 174 CRYST1 61.379 68.558 102.701 90.00 90.00 90.00 P 21 21 21 8 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 0.016292 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009737 0.00000