HEADER ISOMERASE 31-OCT-14 4WUD TITLE N-TERMINAL 43 KDA FRAGMENT OF THE E. COLI DNA GYRASE B SUBUNIT GROWN TITLE 2 FROM NO SALT CONDITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL 43 KDA FRAGMENT, UNP RESIDUES 2-393; COMPND 5 EC: 5.99.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI STRAIN K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: GYRB, ACRB, HIMB, HISU, NALC, PARA, PCBA, B3699, JW5625; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PAJ1 KEYWDS DNA GYRASE, ATPASE DOMAIN, ATPASE ACTIVITY, GHKL SUPERFAMILY, KEYWDS 2 MONOVALENT CATIONS, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.J.HEARNSHAW,T.T.CHUNG,C.E.M.STEVENSON,A.MAXWELL,D.M.LAWSON REVDAT 3 10-JAN-24 4WUD 1 LINK REVDAT 2 22-APR-15 4WUD 1 JRNL REVDAT 1 08-APR-15 4WUD 0 JRNL AUTH S.J.HEARNSHAW,T.T.CHUNG,C.E.M.STEVENSON,A.MAXWELL,D.M.LAWSON JRNL TITL THE ROLE OF MONOVALENT CATIONS IN THE ATPASE REACTION OF DNA JRNL TITL 2 GYRASE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 996 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 25849408 JRNL DOI 10.1107/S1399004715002916 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 34791 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1894 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2512 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.3960 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.4100 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 : 34 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.32000 REMARK 3 B22 (A**2) : 2.53000 REMARK 3 B33 (A**2) : -1.22000 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): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.184 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3026 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2824 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4110 ; 1.343 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6484 ; 0.787 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 388 ; 5.403 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;37.319 ;24.380 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;13.806 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.696 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 463 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3529 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 687 ; 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): 1540 ; 1.487 ; 2.576 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1539 ; 1.488 ; 2.575 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1923 ; 2.134 ; 3.855 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 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 4 A 218 REMARK 3 ORIGIN FOR THE GROUP (A): 17.3660 22.1193 -18.7036 REMARK 3 T TENSOR REMARK 3 T11: 0.0964 T22: 0.0264 REMARK 3 T33: 0.1047 T12: 0.0310 REMARK 3 T13: 0.0572 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 3.4200 L22: 1.1520 REMARK 3 L33: 1.3568 L12: 0.8327 REMARK 3 L13: -0.0922 L23: 0.1349 REMARK 3 S TENSOR REMARK 3 S11: -0.1860 S12: 0.0183 S13: -0.4561 REMARK 3 S21: 0.0460 S22: 0.0909 S23: -0.1685 REMARK 3 S31: 0.1333 S32: 0.1565 S33: 0.0951 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 : A 219 A 299 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1831 48.2124 -3.8136 REMARK 3 T TENSOR REMARK 3 T11: 0.1087 T22: 0.0295 REMARK 3 T33: 0.1184 T12: 0.0263 REMARK 3 T13: -0.0390 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.7313 L22: 6.9085 REMARK 3 L33: 1.5350 L12: 0.2369 REMARK 3 L13: 0.4565 L23: 1.0627 REMARK 3 S TENSOR REMARK 3 S11: -0.0310 S12: 0.0773 S13: 0.2060 REMARK 3 S21: -0.2930 S22: 0.0289 S23: 0.3535 REMARK 3 S31: -0.2175 S32: 0.0535 S33: 0.0020 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 300 A 318 REMARK 3 ORIGIN FOR THE GROUP (A): 1.2491 61.4414 -3.2643 REMARK 3 T TENSOR REMARK 3 T11: 0.7761 T22: 0.3173 REMARK 3 T33: 0.8257 T12: 0.0605 REMARK 3 T13: 0.0210 T23: -0.1108 REMARK 3 L TENSOR REMARK 3 L11: 8.0039 L22: 1.0219 REMARK 3 L33: 8.2806 L12: -2.7315 REMARK 3 L13: -8.1359 L23: 2.8056 REMARK 3 S TENSOR REMARK 3 S11: -0.2191 S12: 1.1047 S13: -0.4265 REMARK 3 S21: 0.2177 S22: -0.3307 S23: 0.3818 REMARK 3 S31: 0.3308 S32: -1.1314 S33: 0.5499 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 319 A 392 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0198 50.3079 -4.4751 REMARK 3 T TENSOR REMARK 3 T11: 0.1156 T22: 0.0497 REMARK 3 T33: 0.2545 T12: 0.0239 REMARK 3 T13: -0.0560 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 0.3010 L22: 3.2850 REMARK 3 L33: 0.8954 L12: -0.3146 REMARK 3 L13: 0.1035 L23: -0.2299 REMARK 3 S TENSOR REMARK 3 S11: -0.0356 S12: -0.0469 S13: 0.0469 REMARK 3 S21: 0.0096 S22: 0.0169 S23: 0.6988 REMARK 3 S31: -0.0958 S32: -0.1647 S33: 0.0187 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4WUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000204520. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.917 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36686 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 27.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.83300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 1EI1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-25% PEG 3350, 2 MM MGCL2, 100 MM REMARK 280 TRIS-HCL PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 40.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.90000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.74000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.90000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.74000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.15000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.90000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 70.74000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.15000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.90000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 70.74000 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -40.15000 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 SER A 2 REMARK 465 ASN A 3 REMARK 465 LYS A 304 REMARK 465 LYS A 305 REMARK 465 ALA A 306 REMARK 465 LYS A 307 REMARK 465 VAL A 308 REMARK 465 ARG A 393 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 LYS A 11 CD CE NZ REMARK 470 GLU A 85 CG CD OE1 OE2 REMARK 470 LYS A 110 CD CE NZ REMARK 470 GLU A 137 CD OE1 OE2 REMARK 470 LYS A 139 CE NZ REMARK 470 GLU A 161 CG CD OE1 OE2 REMARK 470 LYS A 189 CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 ASN A 232 CG OD1 ND2 REMARK 470 GLU A 246 CD OE1 OE2 REMARK 470 LYS A 247 CG CD CE NZ REMARK 470 ARG A 276 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 299 CD CE NZ REMARK 470 SER A 309 OG REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 387 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 390 CD OE1 OE2 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 ARG A 136 NE - CZ - NH1 ANGL. DEV. = -3.3 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 LEU A 115 -19.39 -157.47 REMARK 500 ASN A 178 -83.70 65.91 REMARK 500 HIS A 217 56.75 -152.37 REMARK 500 LYS A 233 -169.85 -115.45 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 46 OD1 REMARK 620 2 ANP A 401 O2G 168.9 REMARK 620 3 ANP A 401 O2B 89.3 93.7 REMARK 620 4 ANP A 401 O2A 105.9 85.1 78.7 REMARK 620 5 HOH A 536 O 81.4 87.8 92.7 168.4 REMARK 620 6 HOH A 537 O 90.6 87.5 174.2 95.8 93.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 103 O REMARK 620 2 ASP A 105 O 91.7 REMARK 620 3 HOH A 527 O 85.3 166.8 REMARK 620 4 HOH A 528 O 96.0 82.2 85.3 REMARK 620 5 HOH A 569 O 96.3 86.8 106.3 163.7 REMARK 620 6 HOH A 609 O 171.7 95.3 88.8 89.4 79.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ANP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 DBREF 4WUD A 2 393 UNP P0AES6 GYRB_ECOLI 2 393 SEQRES 1 A 392 SER ASN SER TYR ASP SER SER SER ILE LYS VAL LEU LYS SEQRES 2 A 392 GLY LEU ASP ALA VAL ARG LYS ARG PRO GLY MET TYR ILE SEQRES 3 A 392 GLY ASP THR ASP ASP GLY THR GLY LEU HIS HIS MET VAL SEQRES 4 A 392 PHE GLU VAL VAL ASP ASN ALA ILE ASP GLU ALA LEU ALA SEQRES 5 A 392 GLY HIS CYS LYS GLU ILE ILE VAL THR ILE HIS ALA ASP SEQRES 6 A 392 ASN SER VAL SER VAL GLN ASP ASP GLY ARG GLY ILE PRO SEQRES 7 A 392 THR GLY ILE HIS PRO GLU GLU GLY VAL SER ALA ALA GLU SEQRES 8 A 392 VAL ILE MET THR VAL LEU HIS ALA GLY GLY LYS PHE ASP SEQRES 9 A 392 ASP ASN SER TYR LYS VAL SER GLY GLY LEU HIS GLY VAL SEQRES 10 A 392 GLY VAL SER VAL VAL ASN ALA LEU SER GLN LYS LEU GLU SEQRES 11 A 392 LEU VAL ILE GLN ARG GLU GLY LYS ILE HIS ARG GLN ILE SEQRES 12 A 392 TYR GLU HIS GLY VAL PRO GLN ALA PRO LEU ALA VAL THR SEQRES 13 A 392 GLY GLU THR GLU LYS THR GLY THR MET VAL ARG PHE TRP SEQRES 14 A 392 PRO SER LEU GLU THR PHE THR ASN VAL THR GLU PHE GLU SEQRES 15 A 392 TYR GLU ILE LEU ALA LYS ARG LEU ARG GLU LEU SER PHE SEQRES 16 A 392 LEU ASN SER GLY VAL SER ILE ARG LEU ARG ASP LYS ARG SEQRES 17 A 392 ASP GLY LYS GLU ASP HIS PHE HIS TYR GLU GLY GLY ILE SEQRES 18 A 392 LYS ALA PHE VAL GLU TYR LEU ASN LYS ASN LYS THR PRO SEQRES 19 A 392 ILE HIS PRO ASN ILE PHE TYR PHE SER THR GLU LYS ASP SEQRES 20 A 392 GLY ILE GLY VAL GLU VAL ALA LEU GLN TRP ASN ASP GLY SEQRES 21 A 392 PHE GLN GLU ASN ILE TYR CYS PHE THR ASN ASN ILE PRO SEQRES 22 A 392 GLN ARG ASP GLY GLY THR HIS LEU ALA GLY PHE ARG ALA SEQRES 23 A 392 ALA MET THR ARG THR LEU ASN ALA TYR MET ASP LYS GLU SEQRES 24 A 392 GLY TYR SER LYS LYS ALA LYS VAL SER ALA THR GLY ASP SEQRES 25 A 392 ASP ALA ARG GLU GLY LEU ILE ALA VAL VAL SER VAL LYS SEQRES 26 A 392 VAL PRO ASP PRO LYS PHE SER SER GLN THR LYS ASP LYS SEQRES 27 A 392 LEU VAL SER SER GLU VAL LYS SER ALA VAL GLU GLN GLN SEQRES 28 A 392 MET ASN GLU LEU LEU ALA GLU TYR LEU LEU GLU ASN PRO SEQRES 29 A 392 THR ASP ALA LYS ILE VAL VAL GLY LYS ILE ILE ASP ALA SEQRES 30 A 392 ALA ARG ALA ARG GLU ALA ALA ARG ARG ALA ARG GLU MET SEQRES 31 A 392 THR ARG HET ANP A 401 31 HET MG A 402 1 HET NA A 403 1 HET CL A 404 1 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 NA NA 1+ FORMUL 5 CL CL 1- FORMUL 6 HOH *139(H2 O) HELIX 1 AA1 ASP A 6 ILE A 10 5 5 HELIX 2 AA2 LEU A 16 ARG A 22 1 7 HELIX 3 AA3 ARG A 22 GLY A 28 1 7 HELIX 4 AA4 GLY A 33 ALA A 53 1 21 HELIX 5 AA5 SER A 89 VAL A 97 1 9 HELIX 6 AA6 VAL A 118 LEU A 126 1 9 HELIX 7 AA7 GLU A 183 ASN A 198 1 16 HELIX 8 AA8 GLY A 220 ASN A 230 1 11 HELIX 9 AA9 GLY A 279 GLU A 300 1 22 HELIX 10 AB1 SER A 342 ASN A 364 1 23 HELIX 11 AB2 ASN A 364 MET A 391 1 28 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 132 O GLN A 143 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 VAL A 71 O VAL A 167 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 5 PHE A 241 LYS A 247 0 SHEET 2 AA3 5 ILE A 250 TRP A 258 -1 O VAL A 252 N THR A 245 SHEET 3 AA3 5 LEU A 319 LYS A 326 -1 O SER A 324 N GLU A 253 SHEET 4 AA3 5 ASN A 265 THR A 270 1 N TYR A 267 O VAL A 323 SHEET 5 AA3 5 ILE A 273 PRO A 274 -1 O ILE A 273 N THR A 270 LINK OD1 ASN A 46 MG MG A 402 1555 1555 2.11 LINK O LYS A 103 NA NA A 403 1555 1555 2.56 LINK O ASP A 105 NA NA A 403 1555 1555 2.65 LINK O2G ANP A 401 MG MG A 402 1555 1555 2.04 LINK O2B ANP A 401 MG MG A 402 1555 1555 2.12 LINK O2A ANP A 401 MG MG A 402 1555 1555 4.61 LINK MG MG A 402 O HOH A 536 1555 1555 2.15 LINK MG MG A 402 O HOH A 537 1555 1555 2.12 LINK NA NA A 403 O HOH A 527 1555 1555 2.40 LINK NA NA A 403 O HOH A 528 1555 1555 2.48 LINK NA NA A 403 O HOH A 569 1555 1555 2.29 LINK NA NA A 403 O HOH A 609 1555 1555 2.44 SITE 1 AC1 29 TYR A 5 ILE A 10 GLU A 42 ASN A 46 SITE 2 AC1 29 GLU A 50 ASP A 73 ILE A 78 ILE A 94 SITE 3 AC1 29 ALA A 100 GLY A 101 GLY A 102 LYS A 103 SITE 4 AC1 29 TYR A 109 GLY A 114 LEU A 115 HIS A 116 SITE 5 AC1 29 GLY A 117 VAL A 118 GLY A 119 VAL A 120 SITE 6 AC1 29 GLN A 335 LYS A 337 MG A 402 HOH A 535 SITE 7 AC1 29 HOH A 536 HOH A 537 HOH A 540 HOH A 544 SITE 8 AC1 29 HOH A 545 SITE 1 AC2 4 ASN A 46 ANP A 401 HOH A 536 HOH A 537 SITE 1 AC3 6 LYS A 103 ASP A 105 HOH A 527 HOH A 528 SITE 2 AC3 6 HOH A 569 HOH A 609 SITE 1 AC4 4 ASP A 6 SER A 7 GLY A 81 ARG A 136 CRYST1 87.800 141.480 80.300 90.00 90.00 90.00 C 2 2 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 0.011390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012453 0.00000