HEADER ISOMERASE 04-FEB-18 5Z9P 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 14-233; COMPND 5 EC: 5.99.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: GYRB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 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 5Z9P 1 LINK REVDAT 1 12-DEC-18 5Z9P 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 63865 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3296 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4181 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 200 REMARK 3 BIN FREE R VALUE : 0.2230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.943 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3006 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2805 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4084 ; 1.191 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6406 ; 0.872 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 370 ; 5.386 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;39.544 ;24.570 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 498 ; 9.585 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;19.020 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 466 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3577 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 700 ; 0.001 ; 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 ; 0.539 ; 1.011 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1488 ; 0.538 ; 1.010 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1856 ; 0.914 ; 1.511 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1857 ; 0.914 ; 1.512 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1517 ; 0.852 ; 1.124 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1518 ; 0.851 ; 1.124 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2229 ; 1.331 ; 1.645 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 13335 ; 2.778 ; 9.931 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 13032 ; 2.588 ; 9.682 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 : NULL 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 5Z9P 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_1300006710. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-16 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 : 67161 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 70.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.07300 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: MOLREP REMARK 200 STARTING MODEL: 4P8O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 8.0, 0.1M MGCL2, REMARK 280 22%(W/V) POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 71.55150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.55150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.83000 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: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 TYR A 14 REMARK 465 GLY A 15 REMARK 465 ALA A 16 REMARK 465 GLY A 17 REMARK 465 GLN A 18 REMARK 465 ILE A 19 REMARK 465 GLY A 231 REMARK 465 GLY A 232 REMARK 465 ILE A 233 REMARK 465 TYR B 14 REMARK 465 GLY B 15 REMARK 465 ALA B 16 REMARK 465 GLY B 17 REMARK 465 GLN B 18 REMARK 465 ILE B 19 REMARK 465 GLN B 20 REMARK 465 VAL B 21 REMARK 465 GLU B 92 REMARK 465 LYS B 93 REMARK 465 MET B 94 REMARK 465 GLY B 231 REMARK 465 GLY B 232 REMARK 465 ILE B 233 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 ARG A 42 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 66 OE1 NE2 REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 GLU A 193 CG CD OE1 OE2 REMARK 470 GLN A 197 CG CD OE1 NE2 REMARK 470 LYS A 207 CD CE NZ REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 LEU B 22 CG CD1 CD2 REMARK 470 GLU B 23 CG CD OE1 OE2 REMARK 470 GLU B 26 CG CD OE1 OE2 REMARK 470 ARG B 31 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 42 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 66 OE1 NE2 REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 LYS B 170 CG CD CE NZ REMARK 470 GLU B 182 CG CD OE1 OE2 REMARK 470 GLN B 197 CG CD OE1 NE2 REMARK 470 GLU B 219 CG CD OE1 OE2 REMARK 470 GLU B 230 CG CD OE1 OE2 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 O HOH B 401 O HOH B 434 2.14 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 THR B 104 C SER B 128 N 0.146 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 ASN A 206 77.52 -114.37 REMARK 500 ASN A 221 86.29 -150.01 REMARK 500 HIS A 228 96.31 -161.09 REMARK 500 HIS B 228 84.89 -157.41 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 54 OD1 REMARK 620 2 HOH A 406 O 86.6 REMARK 620 3 HOH A 495 O 85.5 94.1 REMARK 620 4 HOH A 499 O 89.1 92.6 171.2 REMARK 620 5 HOH A 503 O 174.0 88.5 91.4 94.5 REMARK 620 6 HOH A 541 O 96.1 176.9 84.7 88.9 88.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 54 OD1 REMARK 620 2 HOH B 409 O 78.2 REMARK 620 3 HOH B 468 O 91.8 101.4 REMARK 620 4 HOH B 536 O 89.2 167.3 80.5 REMARK 620 5 HOH B 556 O 161.5 103.2 105.7 88.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AX7 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AX7 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 302 DBREF 5Z9P A 14 233 UNP P0A0K8 GYRB_STAAU 14 233 DBREF 5Z9P B 14 233 UNP P0A0K8 GYRB_STAAU 14 233 SEQADV 5Z9P A UNP P0A0K8 VAL 105 DELETION SEQADV 5Z9P A UNP P0A0K8 LEU 106 DELETION SEQADV 5Z9P A UNP P0A0K8 HIS 107 DELETION SEQADV 5Z9P A UNP P0A0K8 ALA 108 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 109 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 110 DELETION SEQADV 5Z9P A UNP P0A0K8 LYS 111 DELETION SEQADV 5Z9P A UNP P0A0K8 PHE 112 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 113 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 114 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 115 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 116 DELETION SEQADV 5Z9P A UNP P0A0K8 TYR 117 DELETION SEQADV 5Z9P A UNP P0A0K8 LYS 118 DELETION SEQADV 5Z9P A UNP P0A0K8 VAL 119 DELETION SEQADV 5Z9P A UNP P0A0K8 SER 120 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 121 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 122 DELETION SEQADV 5Z9P A UNP P0A0K8 LEU 123 DELETION SEQADV 5Z9P A UNP P0A0K8 HIS 124 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 125 DELETION SEQADV 5Z9P A UNP P0A0K8 VAL 126 DELETION SEQADV 5Z9P A UNP P0A0K8 GLY 127 DELETION SEQADV 5Z9P B UNP P0A0K8 VAL 105 DELETION SEQADV 5Z9P B UNP P0A0K8 LEU 106 DELETION SEQADV 5Z9P B UNP P0A0K8 HIS 107 DELETION SEQADV 5Z9P B UNP P0A0K8 ALA 108 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 109 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 110 DELETION SEQADV 5Z9P B UNP P0A0K8 LYS 111 DELETION SEQADV 5Z9P B UNP P0A0K8 PHE 112 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 113 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 114 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 115 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 116 DELETION SEQADV 5Z9P B UNP P0A0K8 TYR 117 DELETION SEQADV 5Z9P B UNP P0A0K8 LYS 118 DELETION SEQADV 5Z9P B UNP P0A0K8 VAL 119 DELETION SEQADV 5Z9P B UNP P0A0K8 SER 120 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 121 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 122 DELETION SEQADV 5Z9P B UNP P0A0K8 LEU 123 DELETION SEQADV 5Z9P B UNP P0A0K8 HIS 124 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 125 DELETION SEQADV 5Z9P B UNP P0A0K8 VAL 126 DELETION SEQADV 5Z9P B UNP P0A0K8 GLY 127 DELETION SEQRES 1 A 197 TYR GLY ALA GLY GLN ILE GLN VAL LEU GLU GLY LEU GLU SEQRES 2 A 197 ALA VAL ARG LYS ARG PRO GLY MET TYR ILE GLY SER THR SEQRES 3 A 197 SER GLU ARG GLY LEU HIS HIS LEU VAL TRP GLU ILE VAL SEQRES 4 A 197 ASP ASN SER ILE ASP GLU ALA LEU ALA GLY TYR ALA ASN SEQRES 5 A 197 GLN ILE GLU VAL VAL ILE GLU LYS ASP ASN TRP ILE LYS SEQRES 6 A 197 VAL THR ASP ASN GLY ARG GLY ILE PRO VAL ASP ILE GLN SEQRES 7 A 197 GLU LYS MET GLY ARG PRO ALA VAL GLU VAL ILE LEU THR SEQRES 8 A 197 SER SER VAL VAL ASN ALA LEU SER GLN ASP LEU GLU VAL SEQRES 9 A 197 TYR VAL HIS ARG ASN GLU THR ILE TYR HIS GLN ALA TYR SEQRES 10 A 197 LYS LYS GLY VAL PRO GLN PHE ASP LEU LYS GLU VAL GLY SEQRES 11 A 197 THR THR ASP LYS THR GLY THR VAL ILE ARG PHE LYS ALA SEQRES 12 A 197 ASP GLY GLU ILE PHE THR GLU THR THR VAL TYR ASN TYR SEQRES 13 A 197 GLU THR LEU GLN GLN ARG ILE ARG GLU LEU ALA PHE LEU SEQRES 14 A 197 ASN LYS GLY ILE GLN ILE THR LEU ARG ASP GLU ARG ASP SEQRES 15 A 197 GLU GLU ASN VAL ARG GLU ASP SER TYR HIS TYR GLU GLY SEQRES 16 A 197 GLY ILE SEQRES 1 B 197 TYR GLY ALA GLY GLN ILE GLN VAL LEU GLU GLY LEU GLU SEQRES 2 B 197 ALA VAL ARG LYS ARG PRO GLY MET TYR ILE GLY SER THR SEQRES 3 B 197 SER GLU ARG GLY LEU HIS HIS LEU VAL TRP GLU ILE VAL SEQRES 4 B 197 ASP ASN SER ILE ASP GLU ALA LEU ALA GLY TYR ALA ASN SEQRES 5 B 197 GLN ILE GLU VAL VAL ILE GLU LYS ASP ASN TRP ILE LYS SEQRES 6 B 197 VAL THR ASP ASN GLY ARG GLY ILE PRO VAL ASP ILE GLN SEQRES 7 B 197 GLU LYS MET GLY ARG PRO ALA VAL GLU VAL ILE LEU THR SEQRES 8 B 197 SER SER VAL VAL ASN ALA LEU SER GLN ASP LEU GLU VAL SEQRES 9 B 197 TYR VAL HIS ARG ASN GLU THR ILE TYR HIS GLN ALA TYR SEQRES 10 B 197 LYS LYS GLY VAL PRO GLN PHE ASP LEU LYS GLU VAL GLY SEQRES 11 B 197 THR THR ASP LYS THR GLY THR VAL ILE ARG PHE LYS ALA SEQRES 12 B 197 ASP GLY GLU ILE PHE THR GLU THR THR VAL TYR ASN TYR SEQRES 13 B 197 GLU THR LEU GLN GLN ARG ILE ARG GLU LEU ALA PHE LEU SEQRES 14 B 197 ASN LYS GLY ILE GLN ILE THR LEU ARG ASP GLU ARG ASP SEQRES 15 B 197 GLU GLU ASN VAL ARG GLU ASP SER TYR HIS TYR GLU GLY SEQRES 16 B 197 GLY ILE HET AX7 A 301 10 HET MG A 302 1 HET AX7 B 301 10 HET MG B 302 1 HETNAM AX7 1H-BENZIMIDAZOL-2-AMINE HETNAM MG MAGNESIUM ION FORMUL 3 AX7 2(C7 H7 N3) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *350(H2 O) HELIX 1 AA1 GLN A 20 ARG A 31 1 12 HELIX 2 AA2 ARG A 31 GLY A 37 1 7 HELIX 3 AA3 SER A 40 ALA A 61 1 22 HELIX 4 AA4 LYS A 73 ASN A 75 5 3 HELIX 5 AA5 PRO A 97 SER A 128 1 9 HELIX 6 AA6 SER A 129 LEU A 134 1 6 HELIX 7 AA7 ASN A 191 ASN A 206 1 16 HELIX 8 AA8 GLU B 23 ARG B 31 1 9 HELIX 9 AA9 PRO B 32 GLY B 37 1 6 HELIX 10 AB1 SER B 40 ALA B 61 1 22 HELIX 11 AB2 PRO B 97 THR B 104 1 8 HELIX 12 AB3 SER B 129 LEU B 134 1 6 HELIX 13 AB4 ASN B 191 ASN B 206 1 16 SHEET 1 AA1 3 VAL A 157 PRO A 158 0 SHEET 2 AA1 3 THR A 147 LYS A 154 -1 N LYS A 154 O VAL A 157 SHEET 3 AA1 3 LYS A 163 THR A 167 -1 O VAL A 165 N ILE A 148 SHEET 1 AA2 8 VAL A 157 PRO A 158 0 SHEET 2 AA2 8 THR A 147 LYS A 154 -1 N LYS A 154 O VAL A 157 SHEET 3 AA2 8 SER A 135 ARG A 144 -1 N LEU A 138 O TYR A 153 SHEET 4 AA2 8 GLY A 172 ALA A 179 -1 O ARG A 176 N GLU A 139 SHEET 5 AA2 8 TRP A 76 ASP A 81 -1 N VAL A 79 O ILE A 175 SHEET 6 AA2 8 GLN A 66 GLU A 72 -1 N VAL A 70 O LYS A 78 SHEET 7 AA2 8 GLN A 210 ASP A 215 1 O THR A 212 N VAL A 69 SHEET 8 AA2 8 ARG A 223 TYR A 227 -1 O ASP A 225 N LEU A 213 SHEET 1 AA3 3 VAL B 157 PRO B 158 0 SHEET 2 AA3 3 THR B 147 LYS B 154 -1 N LYS B 154 O VAL B 157 SHEET 3 AA3 3 LYS B 163 THR B 167 -1 O VAL B 165 N ILE B 148 SHEET 1 AA4 8 VAL B 157 PRO B 158 0 SHEET 2 AA4 8 THR B 147 LYS B 154 -1 N LYS B 154 O VAL B 157 SHEET 3 AA4 8 SER B 135 ARG B 144 -1 N LEU B 138 O TYR B 153 SHEET 4 AA4 8 GLY B 172 ALA B 179 -1 O GLY B 172 N HIS B 143 SHEET 5 AA4 8 TRP B 76 ASP B 81 -1 N VAL B 79 O ILE B 175 SHEET 6 AA4 8 GLN B 66 GLU B 72 -1 N GLU B 72 O TRP B 76 SHEET 7 AA4 8 GLN B 210 ASP B 215 1 O THR B 212 N VAL B 69 SHEET 8 AA4 8 ARG B 223 TYR B 227 -1 O ASP B 225 N LEU B 213 LINK OD1 ASN A 54 MG MG A 302 1555 1555 2.03 LINK MG MG A 302 O HOH A 406 1555 1555 2.12 LINK MG MG A 302 O HOH A 495 1555 1555 2.14 LINK MG MG A 302 O HOH A 499 1555 1555 2.08 LINK MG MG A 302 O HOH A 503 1555 2758 2.06 LINK MG MG A 302 O HOH A 541 1555 1555 2.09 LINK OD1 ASN B 54 MG MG B 302 1555 1555 2.26 LINK MG MG B 302 O HOH B 409 1555 1555 2.10 LINK MG MG B 302 O HOH B 468 1555 1555 2.05 LINK MG MG B 302 O HOH B 536 1555 1555 2.33 LINK MG MG B 302 O HOH B 556 1555 1555 1.97 SITE 1 AC1 7 ASN A 54 ASP A 81 ILE A 86 ILE A 102 SITE 2 AC1 7 LEU A 103 HOH A 403 HOH A 455 SITE 1 AC2 5 ASN A 54 HOH A 406 HOH A 495 HOH A 499 SITE 2 AC2 5 HOH A 541 SITE 1 AC3 5 ASN B 54 ASP B 81 ILE B 86 ILE B 102 SITE 2 AC3 5 HOH B 404 SITE 1 AC4 5 ASN B 54 HOH B 409 HOH B 468 HOH B 536 SITE 2 AC4 5 HOH B 556 CRYST1 143.103 55.660 51.055 90.00 100.27 90.00 C 1 2 1 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 0.006988 0.000000 0.001267 0.00000 SCALE2 0.000000 0.017966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019906 0.00000