HEADER ISOMERASE 09-AUG-12 4B6C TITLE STRUCTURE OF THE M. SMEGMATIS GYRB ATPASE DOMAIN IN COMPLEX WITH AN TITLE 2 AMINOPYRAZINAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE SUBUNIT B,DNA GYRASE SUBUNIT B,DNA GYRASE COMPND 3 SUBUNIT B; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: ATPASE DOMAIN, RESIDUES 9-102,123-213,246-255,ATPASE COMPND 6 DOMAIN, RESIDUES 9-102,123-213,246-255,ATPASE DOMAIN, RESIDUES 9-102, COMPND 7 123-213,246-255; COMPND 8 EC: 5.99.1.3,5.99.1.3,5.99.1.3; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 1772; SOURCE 4 GENE: GYRB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ISOMERASE, DNA TOPOISOMERASE, INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR J.A.TUCKER,P.S.SHIRUDE,P.MADHAVAPEDDI,S.HUSSEIN,R.BASU,S.GHORPADE REVDAT 5 01-MAY-24 4B6C 1 REMARK LINK REVDAT 4 28-NOV-18 4B6C 1 COMPND SOURCE JRNL DBREF REVDAT 4 2 1 SEQADV REVDAT 3 04-APR-18 4B6C 1 REMARK REVDAT 2 03-APR-13 4B6C 1 COMPND JRNL REVDAT 1 23-JAN-13 4B6C 0 JRNL AUTH P.S.SHIRUDE,P.MADHAVAPEDDI,J.A.TUCKER,K.MURUGAN,V.PATIL, JRNL AUTH 2 H.BASAVARAJAPPA,A.V.RAICHURKAR,V.HUMNABADKAR,S.HUSSEIN, JRNL AUTH 3 S.SHARMA,V.K.RAMYA,C.B.NARAYAN,T.S.BALGANESH, JRNL AUTH 4 V.K.SAMBANDAMURTHY JRNL TITL AMINOPYRAZINAMIDES: NOVEL AND SPECIFIC GYRB INHIBITORS THAT JRNL TITL 2 KILL REPLICATING AND NONREPLICATING MYCOBACTERIUM JRNL TITL 3 TUBERCULOSIS. JRNL REF ACS CHEM. BIOL. V. 8 519 2013 JRNL REFN ESSN 1554-8937 JRNL PMID 23268609 JRNL DOI 10.1021/CB300510W REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 16098 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 815 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.74 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1879 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2030 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1764 REMARK 3 BIN R VALUE (WORKING SET) : 0.1981 REMARK 3 BIN FREE R VALUE : 0.2748 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.12 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 115 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2570 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.73410 REMARK 3 B22 (A**2) : -6.82150 REMARK 3 B33 (A**2) : 3.08740 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.353 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.240 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.338 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.240 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2723 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3699 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 924 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 68 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 403 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2723 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 342 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 3135 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.07 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.07 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.61 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESIDUES 36 - 255 REMARK 3 ORIGIN FOR THE GROUP (A): 21.9409 40.6747 82.3372 REMARK 3 T TENSOR REMARK 3 T11: 0.0562 T22: 0.1630 REMARK 3 T33: -0.0055 T12: -0.0060 REMARK 3 T13: 0.0294 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.7440 L22: 2.4743 REMARK 3 L33: 2.5775 L12: -0.3215 REMARK 3 L13: 0.7069 L23: -0.2642 REMARK 3 S TENSOR REMARK 3 S11: -0.0062 S12: 0.0512 S13: 0.0328 REMARK 3 S21: 0.1034 S22: 0.0254 S23: -0.0890 REMARK 3 S31: 0.1220 S32: 0.2300 S33: -0.0192 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B AND RESIDUES 37 - 255 REMARK 3 ORIGIN FOR THE GROUP (A): 1.6835 24.4647 60.5549 REMARK 3 T TENSOR REMARK 3 T11: 0.0254 T22: 0.0802 REMARK 3 T33: -0.0219 T12: 0.0214 REMARK 3 T13: 0.0083 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 2.6591 L22: 1.1580 REMARK 3 L33: 1.9857 L12: 0.0157 REMARK 3 L13: 0.5647 L23: -1.0302 REMARK 3 S TENSOR REMARK 3 S11: -0.1107 S12: 0.0013 S13: 0.0826 REMARK 3 S21: 0.0122 S22: 0.0587 S23: -0.0127 REMARK 3 S31: -0.0908 S32: -0.0320 S33: 0.0520 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4B6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1290053680. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 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 FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAXHF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16117 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 200 DATA REDUNDANCY : 5.260 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.64 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 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: AMORE REMARK 200 STARTING MODEL: INTERNAL MSM GYRB MODEL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NA ACETATE PH 5.7, 200MM CALCIUM REMARK 280 ACETATE, 19% PEG 8000 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 95.97050 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 95.97050 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 21.72750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.12550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.72750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.12550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 95.97050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.72750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.12550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 95.97050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.72750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.12550 REMARK 290 SMTRY3 8 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 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 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 MET A 8 REMARK 465 PRO A 9 REMARK 465 LYS A 10 REMARK 465 GLU A 11 REMARK 465 TYR A 12 REMARK 465 GLY A 13 REMARK 465 ALA A 14 REMARK 465 ASP A 15 REMARK 465 SER A 16 REMARK 465 ILE A 17 REMARK 465 THR A 18 REMARK 465 ILE A 19 REMARK 465 LEU A 20 REMARK 465 GLU A 21 REMARK 465 GLY A 22 REMARK 465 LEU A 23 REMARK 465 GLU A 24 REMARK 465 ALA A 25 REMARK 465 VAL A 26 REMARK 465 ARG A 27 REMARK 465 LYS A 28 REMARK 465 ARG A 29 REMARK 465 PRO A 30 REMARK 465 GLY A 31 REMARK 465 MET A 32 REMARK 465 TYR A 33 REMARK 465 ILE A 34 REMARK 465 GLY A 35 REMARK 465 GLU A 87 REMARK 465 MET A 88 REMARK 465 HIS A 89 REMARK 465 ALA A 90 REMARK 465 THR A 91 REMARK 465 GLY A 92 REMARK 465 MET A 93 REMARK 465 MET B 8 REMARK 465 PRO B 9 REMARK 465 LYS B 10 REMARK 465 GLU B 11 REMARK 465 TYR B 12 REMARK 465 GLY B 13 REMARK 465 ALA B 14 REMARK 465 ASP B 15 REMARK 465 SER B 16 REMARK 465 ILE B 17 REMARK 465 THR B 18 REMARK 465 ILE B 19 REMARK 465 LEU B 20 REMARK 465 GLU B 21 REMARK 465 GLY B 22 REMARK 465 LEU B 23 REMARK 465 GLU B 24 REMARK 465 ALA B 25 REMARK 465 VAL B 26 REMARK 465 ARG B 27 REMARK 465 LYS B 28 REMARK 465 ARG B 29 REMARK 465 PRO B 30 REMARK 465 GLY B 31 REMARK 465 MET B 32 REMARK 465 TYR B 33 REMARK 465 ILE B 34 REMARK 465 GLY B 35 REMARK 465 SER B 36 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 THR A 95 OG1 CG2 REMARK 470 GLN A 102 CG CD OE1 NE2 REMARK 470 LYS A 157 CG CD CE NZ REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 LYS A 165 CE NZ REMARK 470 GLU A 181 CG CD OE1 OE2 REMARK 470 THR A 182 OG1 CG2 REMARK 470 GLN B 102 CG CD OE1 NE2 REMARK 470 LYS B 165 CD CE NZ REMARK 470 GLU B 178 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 96 60.33 -102.26 REMARK 500 ASP A 97 -9.00 -147.25 REMARK 500 SER A 153 -20.20 76.70 REMARK 500 THR A 182 -58.50 -123.52 REMARK 500 THR A 183 -1.36 53.49 REMARK 500 THR B 91 4.05 -69.03 REMARK 500 VAL B 123 24.68 -73.09 REMARK 500 VAL B 125 -50.82 80.23 REMARK 500 SER B 153 -5.76 76.57 REMARK 500 GLU B 181 -111.28 49.66 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 NA A1257 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 80 O REMARK 620 2 GLY A 81 O 73.8 REMARK 620 3 THR A 167 OG1 142.6 75.0 REMARK 620 4 HOH A2041 O 100.4 125.1 81.2 REMARK 620 5 HOH A2042 O 147.8 137.4 68.1 69.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1257 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 80 O REMARK 620 2 GLY B 81 O 67.1 REMARK 620 3 THR B 167 O 78.9 62.0 REMARK 620 4 THR B 167 OG1 135.0 69.0 72.2 REMARK 620 5 HOH B2010 O 85.3 72.9 134.9 91.2 REMARK 620 6 HOH B2011 O 69.6 119.7 142.3 145.5 63.6 REMARK 620 7 HOH B2043 O 105.8 130.5 68.6 95.0 156.3 100.1 REMARK 620 8 HOH B2044 O 148.6 140.1 124.2 76.0 89.6 80.3 69.9 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 B5U A 1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B5U B 1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1257 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 103-122 DELETED AND RESIDUES 213-246 REPLACED BY REMARK 999 DG TO IMPROVE CRYTALLISABILITY DBREF 4B6C A 9 102 UNP P0C559 GYRB_MYCSM 9 102 DBREF 4B6C A 123 213 UNP P0C559 GYRB_MYCSM 123 213 DBREF 4B6C A 246 255 UNP P0C559 GYRB_MYCSM 246 255 DBREF 4B6C B 9 102 UNP P0C559 GYRB_MYCSM 9 102 DBREF 4B6C B 123 213 UNP P0C559 GYRB_MYCSM 123 213 DBREF 4B6C B 246 255 UNP P0C559 GYRB_MYCSM 246 255 SEQADV 4B6C MET A 8 UNP P0C559 INITIATING METHIONINE SEQADV 4B6C ASP A 213 UNP P0C559 VAL 213 ENGINEERED MUTATION SEQADV 4B6C GLY A 246 UNP P0C559 VAL 246 ENGINEERED MUTATION SEQADV 4B6C MET B 8 UNP P0C559 INITIATING METHIONINE SEQADV 4B6C ASP B 213 UNP P0C559 VAL 213 ENGINEERED MUTATION SEQADV 4B6C GLY B 246 UNP P0C559 VAL 246 ENGINEERED MUTATION SEQRES 1 A 196 MET PRO LYS GLU TYR GLY ALA ASP SER ILE THR ILE LEU SEQRES 2 A 196 GLU GLY LEU GLU ALA VAL ARG LYS ARG PRO GLY MET TYR SEQRES 3 A 196 ILE GLY SER THR GLY GLU ARG GLY LEU HIS HIS LEU ILE SEQRES 4 A 196 TRP GLU VAL VAL ASP ASN ALA VAL ASP GLU ALA MET ALA SEQRES 5 A 196 GLY PHE ALA THR ARG VAL ASP VAL LYS ILE HIS ALA ASP SEQRES 6 A 196 GLY SER VAL GLU VAL ARG ASP ASP GLY ARG GLY ILE PRO SEQRES 7 A 196 VAL GLU MET HIS ALA THR GLY MET PRO THR ILE ASP VAL SEQRES 8 A 196 VAL MET THR GLN VAL GLY VAL SER VAL VAL ASN ALA LEU SEQRES 9 A 196 SER THR ARG LEU GLU ALA THR VAL LEU ARG ASP GLY TYR SEQRES 10 A 196 GLU TRP PHE GLN TYR TYR ASP ARG SER VAL PRO GLY LYS SEQRES 11 A 196 LEU LYS GLN GLY GLY GLU THR LYS GLU THR GLY THR THR SEQRES 12 A 196 ILE ARG PHE TRP ALA ASP PRO GLU ILE PHE GLU THR THR SEQRES 13 A 196 ASP TYR ASN PHE GLU THR VAL ALA ARG ARG LEU GLN GLU SEQRES 14 A 196 MET ALA PHE LEU ASN LYS GLY LEU THR ILE GLU LEU THR SEQRES 15 A 196 ASP GLU ARG ASP GLY LYS HIS ARG VAL PHE HIS TYR PRO SEQRES 16 A 196 GLY SEQRES 1 B 196 MET PRO LYS GLU TYR GLY ALA ASP SER ILE THR ILE LEU SEQRES 2 B 196 GLU GLY LEU GLU ALA VAL ARG LYS ARG PRO GLY MET TYR SEQRES 3 B 196 ILE GLY SER THR GLY GLU ARG GLY LEU HIS HIS LEU ILE SEQRES 4 B 196 TRP GLU VAL VAL ASP ASN ALA VAL ASP GLU ALA MET ALA SEQRES 5 B 196 GLY PHE ALA THR ARG VAL ASP VAL LYS ILE HIS ALA ASP SEQRES 6 B 196 GLY SER VAL GLU VAL ARG ASP ASP GLY ARG GLY ILE PRO SEQRES 7 B 196 VAL GLU MET HIS ALA THR GLY MET PRO THR ILE ASP VAL SEQRES 8 B 196 VAL MET THR GLN VAL GLY VAL SER VAL VAL ASN ALA LEU SEQRES 9 B 196 SER THR ARG LEU GLU ALA THR VAL LEU ARG ASP GLY TYR SEQRES 10 B 196 GLU TRP PHE GLN TYR TYR ASP ARG SER VAL PRO GLY LYS SEQRES 11 B 196 LEU LYS GLN GLY GLY GLU THR LYS GLU THR GLY THR THR SEQRES 12 B 196 ILE ARG PHE TRP ALA ASP PRO GLU ILE PHE GLU THR THR SEQRES 13 B 196 ASP TYR ASN PHE GLU THR VAL ALA ARG ARG LEU GLN GLU SEQRES 14 B 196 MET ALA PHE LEU ASN LYS GLY LEU THR ILE GLU LEU THR SEQRES 15 B 196 ASP GLU ARG ASP GLY LYS HIS ARG VAL PHE HIS TYR PRO SEQRES 16 B 196 GLY HET B5U A1256 35 HET NA A1257 1 HET B5U B1256 35 HET NA B1257 1 HETNAM B5U 6-(3,4-DIMETHYLPHENYL)-3-[[4-[3-(4-METHYLPIPERAZIN-1- HETNAM 2 B5U YL)PROPOXY]PHENYL]AMINO]PYRAZINE-2-CARBOXAMIDE HETNAM NA SODIUM ION FORMUL 3 B5U 2(C27 H34 N6 O2) FORMUL 4 NA 2(NA 1+) FORMUL 7 HOH *112(H2 O) HELIX 1 1 GLY A 38 ALA A 59 1 22 HELIX 2 2 VAL A 99 VAL A 125 1 7 HELIX 3 3 SER A 126 LEU A 131 1 6 HELIX 4 4 ASN A 186 ASN A 201 1 16 HELIX 5 5 GLY B 38 ALA B 59 1 22 HELIX 6 6 PRO B 94 THR B 101 1 8 HELIX 7 7 ASP B 176 GLU B 181 1 6 HELIX 8 8 ASN B 186 ASN B 201 1 16 SHEET 1 AA 2 VAL A 154 PRO A 155 0 SHEET 2 AA 2 TYR A 144 ASP A 151 1 O ASP A 151 N VAL A 154 SHEET 1 AB 2 LYS A 159 GLU A 163 0 SHEET 2 AB 2 TYR A 144 ASP A 151 -1 O GLU A 145 N GLY A 161 SHEET 1 AC 8 HIS A 248 PHE A 251 0 SHEET 2 AC 8 THR A 205 ASP A 210 -1 O ILE A 206 N PHE A 251 SHEET 3 AC 8 ARG A 64 ILE A 69 1 O VAL A 65 N GLU A 207 SHEET 4 AC 8 SER A 74 ASP A 79 -1 O GLU A 76 N LYS A 68 SHEET 5 AC 8 GLY A 168 ALA A 175 -1 O THR A 169 N ASP A 79 SHEET 6 AC 8 SER A 132 ARG A 141 -1 N THR A 133 O TRP A 174 SHEET 7 AC 8 TYR A 144 ASP A 151 -1 O TYR A 144 N ARG A 141 SHEET 8 AC 8 VAL A 154 PRO A 155 1 O VAL A 154 N ASP A 151 SHEET 1 AD 8 HIS A 248 PHE A 251 0 SHEET 2 AD 8 THR A 205 ASP A 210 -1 O ILE A 206 N PHE A 251 SHEET 3 AD 8 ARG A 64 ILE A 69 1 O VAL A 65 N GLU A 207 SHEET 4 AD 8 SER A 74 ASP A 79 -1 O GLU A 76 N LYS A 68 SHEET 5 AD 8 GLY A 168 ALA A 175 -1 O THR A 169 N ASP A 79 SHEET 6 AD 8 SER A 132 ARG A 141 -1 N THR A 133 O TRP A 174 SHEET 7 AD 8 TYR A 144 ASP A 151 -1 O TYR A 144 N ARG A 141 SHEET 8 AD 8 LYS A 159 GLU A 163 -1 O LYS A 159 N PHE A 147 SHEET 1 BA 2 VAL B 154 PRO B 155 0 SHEET 2 BA 2 TYR B 144 ASP B 151 1 O ASP B 151 N VAL B 154 SHEET 1 BB 2 LYS B 159 GLU B 163 0 SHEET 2 BB 2 TYR B 144 ASP B 151 -1 O GLU B 145 N GLY B 161 SHEET 1 BC 8 HIS B 248 PHE B 251 0 SHEET 2 BC 8 THR B 205 ASP B 210 -1 O ILE B 206 N PHE B 251 SHEET 3 BC 8 ARG B 64 ILE B 69 1 O VAL B 65 N GLU B 207 SHEET 4 BC 8 SER B 74 ASP B 79 -1 O GLU B 76 N LYS B 68 SHEET 5 BC 8 GLY B 168 ALA B 175 -1 O THR B 169 N ASP B 79 SHEET 6 BC 8 SER B 132 ARG B 141 -1 N THR B 133 O TRP B 174 SHEET 7 BC 8 TYR B 144 ASP B 151 -1 O TYR B 144 N ARG B 141 SHEET 8 BC 8 VAL B 154 PRO B 155 1 O VAL B 154 N ASP B 151 SHEET 1 BD 8 HIS B 248 PHE B 251 0 SHEET 2 BD 8 THR B 205 ASP B 210 -1 O ILE B 206 N PHE B 251 SHEET 3 BD 8 ARG B 64 ILE B 69 1 O VAL B 65 N GLU B 207 SHEET 4 BD 8 SER B 74 ASP B 79 -1 O GLU B 76 N LYS B 68 SHEET 5 BD 8 GLY B 168 ALA B 175 -1 O THR B 169 N ASP B 79 SHEET 6 BD 8 SER B 132 ARG B 141 -1 N THR B 133 O TRP B 174 SHEET 7 BD 8 TYR B 144 ASP B 151 -1 O TYR B 144 N ARG B 141 SHEET 8 BD 8 LYS B 159 GLU B 163 -1 O LYS B 159 N PHE B 147 LINK O ASP A 80 NA NA A1257 1555 1555 2.38 LINK O GLY A 81 NA NA A1257 1555 1555 2.45 LINK OG1 THR A 167 NA NA A1257 1555 1555 2.31 LINK NA NA A1257 O HOH A2041 1555 1555 3.05 LINK NA NA A1257 O HOH A2042 1555 1555 2.42 LINK O ASP B 80 NA NA B1257 1555 1555 2.57 LINK O GLY B 81 NA NA B1257 1555 1555 2.88 LINK O THR B 167 NA NA B1257 1555 1555 3.04 LINK OG1 THR B 167 NA NA B1257 1555 1555 2.27 LINK NA NA B1257 O HOH B2010 1555 1555 2.42 LINK NA NA B1257 O HOH B2011 1555 1555 2.47 LINK NA NA B1257 O HOH B2043 1555 1555 2.63 LINK NA NA B1257 O HOH B2044 1555 1555 2.42 SITE 1 AC1 17 ASN A 52 GLU A 56 ASP A 79 ARG A 82 SITE 2 AC1 17 GLY A 83 ILE A 84 PRO A 85 ASP A 97 SITE 3 AC1 17 GLN A 102 SER A 126 THR A 169 HOH A2007 SITE 4 AC1 17 HOH A2020 HOH A2030 GLN B 195 PHE B 199 SITE 5 AC1 17 TYR B 253 SITE 1 AC2 17 GLN A 195 TYR A 253 GLU B 48 ASN B 52 SITE 2 AC2 17 GLU B 56 ASP B 79 ARG B 82 GLY B 83 SITE 3 AC2 17 ILE B 84 PRO B 85 THR B 95 VAL B 99 SITE 4 AC2 17 MET B 100 SER B 126 HOH B2004 HOH B2019 SITE 5 AC2 17 HOH B2034 SITE 1 AC3 5 ASP A 80 GLY A 81 THR A 167 HOH A2041 SITE 2 AC3 5 HOH A2042 SITE 1 AC4 7 ASP B 80 GLY B 81 THR B 167 HOH B2010 SITE 2 AC4 7 HOH B2011 HOH B2043 HOH B2044 CRYST1 43.455 82.251 191.941 90.00 90.00 90.00 C 2 2 21 16 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 0.023012 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012158 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005210 0.00000 MTRIX1 1 -0.558500 0.829470 0.007420 -19.27874 1 MTRIX2 1 0.829500 0.558500 0.002760 -16.43661 1 MTRIX3 1 -0.001860 0.007700 -0.999970 142.69847 1