HEADER ISOMERASE/ISOMERASE INHIBITOR 24-JUL-15 5CTX TITLE CRYSTAL STRUCTURE OF THE ATP BINDING DOMAIN OF S. AUREUS GYRB TITLE 2 COMPLEXED WITH A FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE SUBUNIT B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ATP BINDING DOMAIN, UNP RESIDUES 2-234 (DELTA 105-127); 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24 KEYWDS DNA GYRASE, GYRB, FRAGMENT-BASED SCREENING, STRUCTURE-BASED DESIGN, KEYWDS 2 ISOMERASE-ISOMERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.A.ANDERSEN,J.BARKER,R.K.CHENG,J.KAHMANN,B.FELICETTI,M.WOOD, AUTHOR 2 C.SCHEICH,M.MESLEH,J.B.CROSS,J.ZHANG,Q.YANG,B.LIPPA,M.D.RYAN REVDAT 3 27-SEP-23 5CTX 1 REMARK LINK REVDAT 2 17-FEB-16 5CTX 1 AUTHOR REVDAT 1 03-FEB-16 5CTX 0 JRNL AUTH M.F.MESLEH,J.B.CROSS,J.ZHANG,J.KAHMANN,O.A.ANDERSEN, JRNL AUTH 2 J.BARKER,R.K.CHENG,B.FELICETTI,M.WOOD,A.T.HADFIELD, JRNL AUTH 3 C.SCHEICH,T.I.MOY,Q.YANG,J.SHOTWELL,K.NGUYEN,B.LIPPA, JRNL AUTH 4 R.DOLLE,M.D.RYAN JRNL TITL FRAGMENT-BASED DISCOVERY OF DNA GYRASE INHIBITORS TARGETING JRNL TITL 2 THE ATPASE SUBUNIT OF GYRB. JRNL REF BIOORG.MED.CHEM.LETT. V. 26 1314 2016 JRNL REFN ESSN 1464-3405 JRNL PMID 26786695 JRNL DOI 10.1016/J.BMCL.2016.01.009 REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 48976 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2623 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3544 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.3820 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3072 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 351 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 0.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.041 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3304 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3168 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4496 ; 2.047 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7279 ; 1.044 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 413 ; 5.588 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;39.414 ;24.693 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 597 ;13.111 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;20.714 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 502 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3769 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 766 ; 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): 1558 ; 2.263 ; 2.300 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1557 ; 2.262 ; 2.298 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1947 ; 3.368 ; 3.434 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 5CTX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000212148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.7 W8RSSI REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51605 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 45.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.270 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.19 REMARK 200 R MERGE FOR SHELL (I) : 0.29700 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 10.2.35 REMARK 200 STARTING MODEL: 1KZN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40-43% MPD_P1K_P3350, 100 MM MOPS/NA REMARK 280 -HEPES, 100 MM DIVALENTS, PH 7.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 296K 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 71.44600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.82750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.44600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.82750 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 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 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 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 408 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 GLY A 0 REMARK 465 SER A 1 REMARK 465 VAL A 2 REMARK 465 THR A 3 REMARK 465 ALA A 4 REMARK 465 LEU A 5 REMARK 465 SER A 6 REMARK 465 ASP A 7 REMARK 465 VAL A 8 REMARK 465 ASN A 9 REMARK 465 ASN A 10 REMARK 465 THR A 11 REMARK 465 ASP A 12 REMARK 465 ASN A 13 REMARK 465 TYR A 14 REMARK 465 GLY A 15 REMARK 465 GLY A 231 REMARK 465 GLY A 232 REMARK 465 ILE A 233 REMARK 465 LYS A 234 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 465 VAL B 2 REMARK 465 THR B 3 REMARK 465 ALA B 4 REMARK 465 LEU B 5 REMARK 465 SER B 6 REMARK 465 ASP B 7 REMARK 465 VAL B 8 REMARK 465 ASN B 9 REMARK 465 ASN B 10 REMARK 465 THR B 11 REMARK 465 ASP B 12 REMARK 465 ASN B 13 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 GLY B 232 REMARK 465 ILE B 233 REMARK 465 LYS B 234 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 A 402 O HOH A 442 1.96 REMARK 500 NH2 ARG A 223 O HOH A 402 2.05 REMARK 500 OG1 THR B 171 O HOH B 403 2.08 REMARK 500 OD1 ASN B 54 O HOH B 404 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 57 CB - CG - OD1 ANGL. DEV. = -7.4 DEGREES REMARK 500 ASP A 57 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 81 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 161 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 161 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP B 169 CB - CG - OD1 ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG B 198 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 198 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 214 NE - CZ - NH2 ANGL. DEV. = 3.1 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 ASN A 82 40.22 -103.09 REMARK 500 ASN A 206 74.40 -114.86 REMARK 500 LYS B 93 -79.05 -25.33 REMARK 500 ASN B 206 73.99 -114.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 578 DISTANCE = 5.90 ANGSTROMS 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 B 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 484 O REMARK 620 2 ASP B 53 OD1 66.1 REMARK 620 3 ASP B 53 OD2 113.2 49.9 REMARK 620 4 ASP B 57 OD2 114.9 126.5 116.8 REMARK 620 5 HOH B 419 O 64.3 62.8 97.3 70.4 REMARK 620 6 HOH B 429 O 95.3 160.9 144.7 63.9 114.2 REMARK 620 7 HOH B 451 O 101.5 93.9 69.4 133.3 155.8 85.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 164 OE1 REMARK 620 2 GLU B 164 OE1 23.8 REMARK 620 3 GLU B 164 OE2 52.9 39.1 REMARK 620 4 GLU B 219 OE1 3.4 20.4 50.8 REMARK 620 5 GLU B 219 OE2 5.8 18.4 47.7 3.1 REMARK 620 6 HOH B 468 O 6.7 17.2 47.9 3.4 1.7 REMARK 620 7 HOH B 528 O 4.6 22.3 48.5 4.8 4.2 5.9 REMARK 620 8 HOH B 530 O 2.4 21.6 50.8 1.6 3.5 4.4 3.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 55G B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CPH RELATED DB: PDB REMARK 900 RELATED ID: 5CTU RELATED DB: PDB REMARK 900 RELATED ID: 5CTW RELATED DB: PDB REMARK 900 RELATED ID: 5CTY RELATED DB: PDB DBREF 5CTX A 2 234 UNP P0A0K8 GYRB_STAAU 2 234 DBREF 5CTX B 2 234 UNP P0A0K8 GYRB_STAAU 2 234 SEQADV 5CTX GLY A 0 UNP P0A0K8 EXPRESSION TAG SEQADV 5CTX SER A 1 UNP P0A0K8 EXPRESSION TAG SEQADV 5CTX A UNP P0A0K8 VAL 105 DELETION SEQADV 5CTX A UNP P0A0K8 LEU 106 DELETION SEQADV 5CTX A UNP P0A0K8 HIS 107 DELETION SEQADV 5CTX A UNP P0A0K8 ALA 108 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 109 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 110 DELETION SEQADV 5CTX A UNP P0A0K8 LYS 111 DELETION SEQADV 5CTX A UNP P0A0K8 PHE 112 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 113 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 114 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 115 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 116 DELETION SEQADV 5CTX A UNP P0A0K8 TYR 117 DELETION SEQADV 5CTX A UNP P0A0K8 LYS 118 DELETION SEQADV 5CTX A UNP P0A0K8 VAL 119 DELETION SEQADV 5CTX A UNP P0A0K8 SER 120 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 121 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 122 DELETION SEQADV 5CTX A UNP P0A0K8 LEU 123 DELETION SEQADV 5CTX A UNP P0A0K8 HIS 124 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 125 DELETION SEQADV 5CTX A UNP P0A0K8 VAL 126 DELETION SEQADV 5CTX A UNP P0A0K8 GLY 127 DELETION SEQADV 5CTX GLY B 0 UNP P0A0K8 EXPRESSION TAG SEQADV 5CTX SER B 1 UNP P0A0K8 EXPRESSION TAG SEQADV 5CTX B UNP P0A0K8 VAL 105 DELETION SEQADV 5CTX B UNP P0A0K8 LEU 106 DELETION SEQADV 5CTX B UNP P0A0K8 HIS 107 DELETION SEQADV 5CTX B UNP P0A0K8 ALA 108 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 109 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 110 DELETION SEQADV 5CTX B UNP P0A0K8 LYS 111 DELETION SEQADV 5CTX B UNP P0A0K8 PHE 112 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 113 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 114 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 115 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 116 DELETION SEQADV 5CTX B UNP P0A0K8 TYR 117 DELETION SEQADV 5CTX B UNP P0A0K8 LYS 118 DELETION SEQADV 5CTX B UNP P0A0K8 VAL 119 DELETION SEQADV 5CTX B UNP P0A0K8 SER 120 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 121 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 122 DELETION SEQADV 5CTX B UNP P0A0K8 LEU 123 DELETION SEQADV 5CTX B UNP P0A0K8 HIS 124 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 125 DELETION SEQADV 5CTX B UNP P0A0K8 VAL 126 DELETION SEQADV 5CTX B UNP P0A0K8 GLY 127 DELETION SEQRES 1 A 212 GLY SER VAL THR ALA LEU SER ASP VAL ASN ASN THR ASP SEQRES 2 A 212 ASN TYR GLY ALA GLY GLN ILE GLN VAL LEU GLU GLY LEU SEQRES 3 A 212 GLU ALA VAL ARG LYS ARG PRO GLY MET TYR ILE GLY SER SEQRES 4 A 212 THR SER GLU ARG GLY LEU HIS HIS LEU VAL TRP GLU ILE SEQRES 5 A 212 VAL ASP ASN SER ILE ASP GLU ALA LEU ALA GLY TYR ALA SEQRES 6 A 212 ASN GLN ILE GLU VAL VAL ILE GLU LYS ASP ASN TRP ILE SEQRES 7 A 212 LYS VAL THR ASP ASN GLY ARG GLY ILE PRO VAL ASP ILE SEQRES 8 A 212 GLN GLU LYS MET GLY ARG PRO ALA VAL GLU VAL ILE LEU SEQRES 9 A 212 THR SER SER VAL VAL ASN ALA LEU SER GLN ASP LEU GLU SEQRES 10 A 212 VAL TYR VAL HIS ARG ASN GLU THR ILE TYR HIS GLN ALA SEQRES 11 A 212 TYR LYS LYS GLY VAL PRO GLN PHE ASP LEU LYS GLU VAL SEQRES 12 A 212 GLY THR THR ASP LYS THR GLY THR VAL ILE ARG PHE LYS SEQRES 13 A 212 ALA ASP GLY GLU ILE PHE THR GLU THR THR VAL TYR ASN SEQRES 14 A 212 TYR GLU THR LEU GLN GLN ARG ILE ARG GLU LEU ALA PHE SEQRES 15 A 212 LEU ASN LYS GLY ILE GLN ILE THR LEU ARG ASP GLU ARG SEQRES 16 A 212 ASP GLU GLU ASN VAL ARG GLU ASP SER TYR HIS TYR GLU SEQRES 17 A 212 GLY GLY ILE LYS SEQRES 1 B 212 GLY SER VAL THR ALA LEU SER ASP VAL ASN ASN THR ASP SEQRES 2 B 212 ASN TYR GLY ALA GLY GLN ILE GLN VAL LEU GLU GLY LEU SEQRES 3 B 212 GLU ALA VAL ARG LYS ARG PRO GLY MET TYR ILE GLY SER SEQRES 4 B 212 THR SER GLU ARG GLY LEU HIS HIS LEU VAL TRP GLU ILE SEQRES 5 B 212 VAL ASP ASN SER ILE ASP GLU ALA LEU ALA GLY TYR ALA SEQRES 6 B 212 ASN GLN ILE GLU VAL VAL ILE GLU LYS ASP ASN TRP ILE SEQRES 7 B 212 LYS VAL THR ASP ASN GLY ARG GLY ILE PRO VAL ASP ILE SEQRES 8 B 212 GLN GLU LYS MET GLY ARG PRO ALA VAL GLU VAL ILE LEU SEQRES 9 B 212 THR SER SER VAL VAL ASN ALA LEU SER GLN ASP LEU GLU SEQRES 10 B 212 VAL TYR VAL HIS ARG ASN GLU THR ILE TYR HIS GLN ALA SEQRES 11 B 212 TYR LYS LYS GLY VAL PRO GLN PHE ASP LEU LYS GLU VAL SEQRES 12 B 212 GLY THR THR ASP LYS THR GLY THR VAL ILE ARG PHE LYS SEQRES 13 B 212 ALA ASP GLY GLU ILE PHE THR GLU THR THR VAL TYR ASN SEQRES 14 B 212 TYR GLU THR LEU GLN GLN ARG ILE ARG GLU LEU ALA PHE SEQRES 15 B 212 LEU ASN LYS GLY ILE GLN ILE THR LEU ARG ASP GLU ARG SEQRES 16 B 212 ASP GLU GLU ASN VAL ARG GLU ASP SER TYR HIS TYR GLU SEQRES 17 B 212 GLY GLY ILE LYS HET MPD A 301 8 HET MPD A 302 8 HET MPD B 301 8 HET MPD B 302 8 HET 55G B 303 27 HET MG B 304 1 HET MG B 305 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM 55G 4-PHENYL-3-[2-(PYRIDIN-3-YL)-1,3-THIAZOL-5-YL]-2,7- HETNAM 2 55G DIHYDRO-6H-PYRAZOLO[3,4-B]PYRIDIN-6-ONE HETNAM MG MAGNESIUM ION FORMUL 3 MPD 4(C6 H14 O2) FORMUL 7 55G C20 H13 N5 O S FORMUL 8 MG 2(MG 2+) FORMUL 10 HOH *351(H2 O) HELIX 1 AA1 ALA A 16 ARG A 31 1 16 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 VAL B 21 ARG B 31 1 11 HELIX 9 AA9 ARG B 31 GLY B 37 1 7 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 HIS A 228 -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 ARG B 176 N GLU B 139 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 ILE B 71 -1 N VAL B 70 O LYS B 78 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 O HOH A 484 MG MG B 304 2556 1555 2.62 LINK OD1BASP B 53 MG MG B 304 1555 1555 2.62 LINK OD2BASP B 53 MG MG B 304 1555 1555 2.52 LINK OD2 ASP B 57 MG MG B 304 1555 1555 2.56 LINK OE1AGLU B 164 MG MG B 305 1555 4546 2.45 LINK OE1BGLU B 164 MG MG B 305 1555 4546 2.60 LINK OE2AGLU B 164 MG MG B 305 1555 4546 2.45 LINK OE1 GLU B 219 MG MG B 305 1555 1555 2.34 LINK OE2 GLU B 219 MG MG B 305 1555 1555 2.56 LINK MG MG B 304 O HOH B 419 1555 1555 2.15 LINK MG MG B 304 O HOH B 429 1555 1555 2.35 LINK MG MG B 304 O HOH B 451 1555 1555 2.21 LINK MG MG B 305 O HOH B 468 1555 1555 2.20 LINK MG MG B 305 O HOH B 528 1555 4556 2.27 LINK MG MG B 305 O HOH B 530 1555 1555 2.20 SITE 1 AC1 6 ASP A 81 HIS A 143 LYS A 170 THR A 171 SITE 2 AC1 6 MPD A 302 HOH A 404 SITE 1 AC2 3 TYR A 141 HIS A 143 MPD A 301 SITE 1 AC3 6 THR B 80 ASP B 81 HIS B 143 LYS B 170 SITE 2 AC3 6 MPD B 302 HOH B 414 SITE 1 AC4 4 TYR B 141 HIS B 143 GLU B 186 MPD B 301 SITE 1 AC5 13 THR A 185 ASN B 54 GLU B 58 ASP B 81 SITE 2 AC5 13 ARG B 84 GLY B 85 PRO B 87 ILE B 102 SITE 3 AC5 13 ARG B 144 ILE B 175 HOH B 424 HOH B 449 SITE 4 AC5 13 HOH B 467 SITE 1 AC6 6 HOH A 484 ASP B 53 ASP B 57 HOH B 419 SITE 2 AC6 6 HOH B 429 HOH B 451 SITE 1 AC7 5 GLU B 164 GLU B 219 HOH B 468 HOH B 528 SITE 2 AC7 5 HOH B 530 CRYST1 142.892 55.655 51.213 90.00 100.55 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 0.006998 0.000000 0.001303 0.00000 SCALE2 0.000000 0.017968 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019862 0.00000