HEADER ISOMERASE 06-MAR-14 4PRX TITLE E. COLI GYRB 43-KDA N-TERMINAL FRAGMENT IN COMPLEX WITH ADP+PI COMPND MOL_ID: 1; COMPND 2 MOLECULE: GYRB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-392; COMPND 5 EC: 5.99.1.3; COMPND 6 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSFDUET1 KEYWDS GYRB, ATP HYDROLYSIS, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.V.STANGER,T.SCHIRMER REVDAT 3 08-NOV-23 4PRX 1 REMARK SEQADV LINK REVDAT 2 22-NOV-17 4PRX 1 REMARK REVDAT 1 24-SEP-14 4PRX 0 JRNL AUTH F.V.STANGER,C.DEHIO,T.SCHIRMER JRNL TITL STRUCTURE OF THE N-TERMINAL GYRASE B FRAGMENT IN COMPLEX JRNL TITL 2 WITH ADPPI REVEALS RIGID-BODY MOTION INDUCED BY ATP JRNL TITL 3 HYDROLYSIS JRNL REF PLOS ONE V. 9 07289 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 25202966 JRNL DOI 10.1371/JOURNAL.PONE.0107289 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 44052 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1986 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) : 2983 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 237 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.73000 REMARK 3 B22 (A**2) : -0.98000 REMARK 3 B33 (A**2) : -0.75000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.106 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2881 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2678 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3915 ; 2.000 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6154 ; 0.893 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 5.919 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;37.877 ;24.806 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 464 ;12.413 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;17.818 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 441 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3303 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 647 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4PRX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44052 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1800 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) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.94800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.1 REMARK 200 STARTING MODEL: 1EI1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRI-AMMONIUM CITRATE PH 6.5, REMARK 280 25%(W/V) PEG2000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K 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 46.19500 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 46.19500 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 38.82000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.82500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.82000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.82500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 46.19500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.82000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.82500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.19500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.82000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.82500 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: 6630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 -46.19500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 576 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 630 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 677 LIES ON A SPECIAL POSITION. 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 MET A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 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 SER A 309 REMARK 465 ALA A 310 REMARK 465 THR A 311 REMARK 465 GLY A 312 REMARK 465 ASP A 313 REMARK 465 ASP A 314 REMARK 465 ALA A 378 REMARK 465 ALA A 379 REMARK 465 ARG A 380 REMARK 465 ALA A 381 REMARK 465 ARG A 382 REMARK 465 GLU A 383 REMARK 465 ALA A 384 REMARK 465 ALA A 385 REMARK 465 ARG A 386 REMARK 465 ARG A 387 REMARK 465 ALA A 388 REMARK 465 ARG A 389 REMARK 465 GLU A 390 REMARK 465 MET A 391 REMARK 465 THR A 392 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 14 CG CD CE NZ REMARK 470 LYS A 57 CE NZ REMARK 470 GLU A 85 CG CD OE1 OE2 REMARK 470 LYS A 110 CD CE NZ REMARK 470 LYS A 212 CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS A 247 CG CD CE NZ REMARK 470 GLN A 263 CG CD OE1 NE2 REMARK 470 ARG A 276 CD NE CZ NH1 NH2 REMARK 470 LYS A 299 CG CD CE NZ REMARK 470 GLU A 300 CG CD OE1 OE2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 351 CG CD OE1 NE2 REMARK 470 LEU A 362 CG CD1 CD2 REMARK 470 LYS A 369 CG CD CE NZ REMARK 470 ASP A 377 CG OD1 OD2 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 HE2 HIS A 37 H GLU A 183 1.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 H TYR A 242 HO1 GOL A 404 8445 1.34 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 -40.12 -137.35 REMARK 500 ASN A 178 -88.75 71.07 REMARK 500 HIS A 217 55.62 -151.69 REMARK 500 LYS A 233 -167.83 -117.88 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 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 46 OD1 REMARK 620 2 ADP A 401 O2B 77.6 REMARK 620 3 ADP A 401 O2A 84.6 79.8 REMARK 620 4 HOH A 642 O 80.5 154.2 111.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EI1 RELATED DB: PDB REMARK 900 GYRB IN COMPLEX WITH AMPPNP REMARK 900 RELATED ID: 4PRV RELATED DB: PDB REMARK 900 GYRB IN COMPLEX WITH ADP REMARK 900 RELATED ID: 4PU9 RELATED DB: PDB REMARK 900 RELATED ID: 4R1F RELATED DB: PDB DBREF 4PRX A 2 392 UNP P0AES6 GYRB_ECOLI 2 392 SEQADV 4PRX MET A -5 UNP P0AES6 EXPRESSION TAG SEQADV 4PRX HIS A -4 UNP P0AES6 EXPRESSION TAG SEQADV 4PRX HIS A -3 UNP P0AES6 EXPRESSION TAG SEQADV 4PRX HIS A -2 UNP P0AES6 EXPRESSION TAG SEQADV 4PRX HIS A -1 UNP P0AES6 EXPRESSION TAG SEQADV 4PRX HIS A 0 UNP P0AES6 EXPRESSION TAG SEQADV 4PRX HIS A 1 UNP P0AES6 EXPRESSION TAG SEQRES 1 A 398 MET HIS HIS HIS HIS HIS HIS SER ASN SER TYR ASP SER SEQRES 2 A 398 SER SER ILE LYS VAL LEU LYS GLY LEU ASP ALA VAL ARG SEQRES 3 A 398 LYS ARG PRO GLY MET TYR ILE GLY ASP THR ASP ASP GLY SEQRES 4 A 398 THR GLY LEU HIS HIS MET VAL PHE GLU VAL VAL ASP ASN SEQRES 5 A 398 ALA ILE ASP GLU ALA LEU ALA GLY HIS CYS LYS GLU ILE SEQRES 6 A 398 ILE VAL THR ILE HIS ALA ASP ASN SER VAL SER VAL GLN SEQRES 7 A 398 ASP ASP GLY ARG GLY ILE PRO THR GLY ILE HIS PRO GLU SEQRES 8 A 398 GLU GLY VAL SER ALA ALA GLU VAL ILE MET THR VAL LEU SEQRES 9 A 398 HIS ALA GLY GLY LYS PHE ASP ASP ASN SER TYR LYS VAL SEQRES 10 A 398 SER GLY GLY LEU HIS GLY VAL GLY VAL SER VAL VAL ASN SEQRES 11 A 398 ALA LEU SER GLN LYS LEU GLU LEU VAL ILE GLN ARG GLU SEQRES 12 A 398 GLY LYS ILE HIS ARG GLN ILE TYR GLU HIS GLY VAL PRO SEQRES 13 A 398 GLN ALA PRO LEU ALA VAL THR GLY GLU THR GLU LYS THR SEQRES 14 A 398 GLY THR MET VAL ARG PHE TRP PRO SER LEU GLU THR PHE SEQRES 15 A 398 THR ASN VAL THR GLU PHE GLU TYR GLU ILE LEU ALA LYS SEQRES 16 A 398 ARG LEU ARG GLU LEU SER PHE LEU ASN SER GLY VAL SER SEQRES 17 A 398 ILE ARG LEU ARG ASP LYS ARG ASP GLY LYS GLU ASP HIS SEQRES 18 A 398 PHE HIS TYR GLU GLY GLY ILE LYS ALA PHE VAL GLU TYR SEQRES 19 A 398 LEU ASN LYS ASN LYS THR PRO ILE HIS PRO ASN ILE PHE SEQRES 20 A 398 TYR PHE SER THR GLU LYS ASP GLY ILE GLY VAL GLU VAL SEQRES 21 A 398 ALA LEU GLN TRP ASN ASP GLY PHE GLN GLU ASN ILE TYR SEQRES 22 A 398 CYS PHE THR ASN ASN ILE PRO GLN ARG ASP GLY GLY THR SEQRES 23 A 398 HIS LEU ALA GLY PHE ARG ALA ALA MET THR ARG THR LEU SEQRES 24 A 398 ASN ALA TYR MET ASP LYS GLU GLY TYR SER LYS LYS ALA SEQRES 25 A 398 LYS VAL SER ALA THR GLY ASP ASP ALA ARG GLU GLY LEU SEQRES 26 A 398 ILE ALA VAL VAL SER VAL LYS VAL PRO ASP PRO LYS PHE SEQRES 27 A 398 SER SER GLN THR LYS ASP LYS LEU VAL SER SER GLU VAL SEQRES 28 A 398 LYS SER ALA VAL GLU GLN GLN MET ASN GLU LEU LEU ALA SEQRES 29 A 398 GLU TYR LEU LEU GLU ASN PRO THR ASP ALA LYS ILE VAL SEQRES 30 A 398 VAL GLY LYS ILE ILE ASP ALA ALA ARG ALA ARG GLU ALA SEQRES 31 A 398 ALA ARG ARG ALA ARG GLU MET THR HET ADP A 401 39 HET PO4 A 402 5 HET MG A 403 1 HET GOL A 404 14 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 PO4 O4 P 3- FORMUL 4 MG MG 2+ FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *237(H2 O) HELIX 1 1 ASP A 6 ILE A 10 5 5 HELIX 2 2 LEU A 16 ARG A 22 1 7 HELIX 3 3 ARG A 22 ILE A 27 1 6 HELIX 4 4 GLY A 33 ALA A 53 1 21 HELIX 5 5 SER A 89 VAL A 97 1 9 HELIX 6 6 VAL A 118 LEU A 126 1 9 HELIX 7 7 GLU A 183 ASN A 198 1 16 HELIX 8 8 GLY A 220 LYS A 231 1 12 HELIX 9 9 GLY A 279 GLU A 300 1 22 HELIX 10 10 SER A 342 ASN A 364 1 23 HELIX 11 11 ASN A 364 ASP A 377 1 14 SHEET 1 A 3 VAL A 149 PRO A 150 0 SHEET 2 A 3 LYS A 139 GLU A 146 -1 N GLU A 146 O VAL A 149 SHEET 3 A 3 ALA A 155 GLU A 159 -1 O THR A 157 N ILE A 140 SHEET 1 B 8 VAL A 149 PRO A 150 0 SHEET 2 B 8 LYS A 139 GLU A 146 -1 N GLU A 146 O VAL A 149 SHEET 3 B 8 SER A 127 ARG A 136 -1 N LEU A 132 O GLN A 143 SHEET 4 B 8 GLY A 164 PRO A 171 -1 O ARG A 168 N GLU A 131 SHEET 5 B 8 VAL A 69 ASP A 73 -1 N VAL A 69 O PHE A 169 SHEET 6 B 8 GLU A 58 ILE A 63 -1 N ILE A 60 O GLN A 72 SHEET 7 B 8 SER A 202 ASP A 207 1 O ARG A 204 N VAL A 61 SHEET 8 B 8 GLU A 213 PHE A 216 -1 O PHE A 216 N ILE A 203 SHEET 1 C 5 PHE A 241 LYS A 247 0 SHEET 2 C 5 ILE A 250 TRP A 258 -1 O VAL A 252 N THR A 245 SHEET 3 C 5 LEU A 319 LYS A 326 -1 O SER A 324 N GLU A 253 SHEET 4 C 5 GLU A 264 THR A 270 1 N TYR A 267 O ALA A 321 SHEET 5 C 5 ILE A 273 PRO A 274 -1 O ILE A 273 N THR A 270 LINK OD1 ASN A 46 MG MG A 403 1555 1555 2.68 LINK O2B ADP A 401 MG MG A 403 1555 1555 2.46 LINK O2A ADP A 401 MG MG A 403 1555 1555 2.61 LINK MG MG A 403 O HOH A 642 1555 1555 2.47 SITE 1 AC1 27 TYR A 5 ILE A 10 ASN A 46 GLU A 50 SITE 2 AC1 27 ASP A 73 ILE A 78 ILE A 94 ALA A 100 SITE 3 AC1 27 GLY A 101 GLY A 102 LYS A 103 TYR A 109 SITE 4 AC1 27 GLY A 114 LEU A 115 HIS A 116 GLY A 117 SITE 5 AC1 27 VAL A 118 GLY A 119 VAL A 120 THR A 165 SITE 6 AC1 27 PO4 A 402 MG A 403 HOH A 502 HOH A 504 SITE 7 AC1 27 HOH A 505 HOH A 511 HOH A 535 SITE 1 AC2 11 GLU A 42 LEU A 115 HIS A 116 GLY A 117 SITE 2 AC2 11 VAL A 118 GLY A 119 LYS A 337 ADP A 401 SITE 3 AC2 11 MG A 403 HOH A 543 HOH A 646 SITE 1 AC3 4 ASN A 46 ADP A 401 PO4 A 402 HOH A 642 SITE 1 AC4 9 TRP A 170 LYS A 223 ASN A 239 ILE A 240 SITE 2 AC4 9 PHE A 241 TYR A 242 HOH A 563 HOH A 575 SITE 3 AC4 9 HOH A 587 CRYST1 77.640 131.650 92.390 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 0.012880 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010824 0.00000