HEADER ISOMERASE 17-JUL-20 6ZT3 TITLE N-TERMINAL 47 KDA FRAGMENT OF THE MYCOBACTERIUM SMEGMATIS DNA GYRASE B TITLE 2 SUBUNIT COMPLEXED WITH ADPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 EC: 5.99.1.3; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RESIDUES 1-427 OF THE WILD-TYPE SEQUENCE WITH A SERINE COMPND 7 RESIDUE APPENDED TO THE N-TERMINUS LEFT AFTER CLEAVAGE OF THE COMPND 8 AFFINITY TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS (STRAIN ATCC 700084 SOURCE 3 / MC(2)155); SOURCE 4 ORGANISM_TAXID: 246196; SOURCE 5 STRAIN: ATCC 700084 / MC(2)155; SOURCE 6 GENE: GYRB, MSMEG_0005, MSMEI_0007; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TYPE IIA TOPOISOMERASE, ATPASE DOMAIN, GHKL SUPERFAMILY, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.FENG,J.E.A.MUNDY,C.E.M.STEVENSON,L.A.MITCHENALL,D.M.LAWSON,K.MI, AUTHOR 2 A.MAXWELL REVDAT 3 31-JAN-24 6ZT3 1 REMARK REVDAT 2 21-APR-21 6ZT3 1 JRNL REVDAT 1 03-MAR-21 6ZT3 0 JRNL AUTH L.FENG,J.E.A.MUNDY,C.E.M.STEVENSON,L.A.MITCHENALL, JRNL AUTH 2 D.M.LAWSON,K.MI,A.MAXWELL JRNL TITL THE PENTAPEPTIDE-REPEAT PROTEIN, MFPA, INTERACTS WITH JRNL TITL 2 MYCOBACTERIAL DNA GYRASE AS A DNA T-SEGMENT MIMIC. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33836580 JRNL DOI 10.1073/PNAS.2016705118 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 63082 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3287 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) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4566 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 247 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3033 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.84000 REMARK 3 B22 (A**2) : -1.84000 REMARK 3 B33 (A**2) : 5.98000 REMARK 3 B12 (A**2) : -0.92000 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): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.159 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3264 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2955 ; 0.007 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4436 ; 1.368 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6855 ; 1.440 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 418 ; 6.279 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 175 ;32.840 ;22.629 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 536 ;15.125 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;18.378 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 427 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3759 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 687 ; 0.002 ; 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): 6218 ; 3.043 ; 3.000 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 6ZT3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66509 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 65.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 38.80 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 39.50 REMARK 200 R MERGE FOR SHELL (I) : 2.48600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.82 REMARK 200 STARTING MODEL: 3ZKB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL, PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 87.15867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 174.31733 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 130.73800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 217.89667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.57933 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 87.15867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 174.31733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 217.89667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 130.73800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 43.57933 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: 11180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 0.500000 0.866025 0.000000 38.49250 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -66.67097 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 43.57933 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 NA NA A 510 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 THR A 214 REMARK 465 ALA A 215 REMARK 465 GLU A 216 REMARK 465 GLU A 217 REMARK 465 VAL A 218 REMARK 465 VAL A 219 REMARK 465 ASP A 220 REMARK 465 ASP A 221 REMARK 465 VAL A 222 REMARK 465 VAL A 223 REMARK 465 LYS A 224 REMARK 465 ASP A 225 REMARK 465 THR A 226 REMARK 465 ALA A 227 REMARK 465 GLU A 228 REMARK 465 ALA A 229 REMARK 465 PRO A 230 REMARK 465 LYS A 231 REMARK 465 THR A 232 REMARK 465 ALA A 233 REMARK 465 ASP A 234 REMARK 465 GLU A 235 REMARK 465 LYS A 236 REMARK 465 ALA A 237 REMARK 465 ALA A 238 REMARK 465 GLU A 239 REMARK 465 ALA A 240 REMARK 465 THR A 241 REMARK 465 GLY A 242 REMARK 465 PRO A 243 REMARK 465 SER A 244 REMARK 465 LYS A 245 REMARK 465 LEU A 426 REMARK 465 VAL A 427 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 5 CG CD CE NZ REMARK 470 LYS A 10 CG CD CE NZ REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 ARG A 40 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 213 CG1 CG2 REMARK 470 LYS A 281 CD CE NZ REMARK 470 GLU A 425 CG CD OE1 OE2 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 CB ALA A 416 CB ALA A 420 12545 1.94 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 120 -15.10 -158.00 REMARK 500 SER A 153 -10.85 85.62 REMARK 500 THR A 269 88.64 65.87 REMARK 500 THR A 307 -16.46 81.75 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 A 895 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 896 DISTANCE = 7.98 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 NA A 510 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 5 O REMARK 620 2 LYS A 5 O 0.0 REMARK 620 3 ASN A 7 OD1 87.8 87.8 REMARK 620 4 ASN A 7 OD1 87.8 87.8 0.0 REMARK 620 5 HOH A 825 O 94.6 94.6 107.5 107.5 REMARK 620 6 HOH A 825 O 171.6 171.6 84.1 84.1 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 52 OD1 REMARK 620 2 ANP A 501 O3G 167.7 REMARK 620 3 ANP A 501 O2B 89.5 90.1 REMARK 620 4 ANP A 501 O2A 93.4 98.8 86.0 REMARK 620 5 HOH A 629 O 90.7 91.2 173.3 87.4 REMARK 620 6 HOH A 705 O 80.1 87.6 94.4 173.6 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 509 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 80 O REMARK 620 2 GLY A 81 O 85.9 REMARK 620 3 THR A 167 O 92.6 77.6 REMARK 620 4 THR A 167 OG1 172.8 89.3 81.1 REMARK 620 5 HOH A 836 O 85.0 170.5 105.6 100.0 REMARK 620 6 HOH A 847 O 91.7 84.7 161.4 93.2 92.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 511 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 99 O REMARK 620 2 ALA A 105 O 131.3 REMARK 620 3 GLY A 122 O 131.2 68.9 REMARK 620 4 SER A 126 OG 65.3 142.7 76.5 REMARK 620 5 ANP A 501 O1A 110.2 110.2 96.2 86.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 511 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 99 O REMARK 620 2 GLN A 102 O 102.5 REMARK 620 3 GLY A 122 O 157.4 96.3 REMARK 620 4 SER A 126 OG 91.7 102.1 96.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 508 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 108 O REMARK 620 2 ASP A 110 O 93.0 REMARK 620 3 HOH A 640 O 86.2 91.8 REMARK 620 4 HOH A 648 O 175.1 91.8 95.0 REMARK 620 5 HOH A 717 O 91.0 83.9 174.8 88.2 REMARK 620 6 HOH A 855 O 80.2 168.0 97.6 94.9 86.3 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 511 DBREF 6ZT3 A 1 427 UNP A0QNE0 GYRB_MYCS2 1 427 SEQADV 6ZT3 SER A 0 UNP A0QNE0 EXPRESSION TAG SEQRES 1 A 428 SER MET ALA ALA GLN LYS ASN ASN ALA PRO LYS GLU TYR SEQRES 2 A 428 GLY ALA ASP SER ILE THR ILE LEU GLU GLY LEU GLU ALA SEQRES 3 A 428 VAL ARG LYS ARG PRO GLY MET TYR ILE GLY SER THR GLY SEQRES 4 A 428 GLU ARG GLY LEU HIS HIS LEU ILE TRP GLU VAL VAL ASP SEQRES 5 A 428 ASN ALA VAL ASP GLU ALA MET ALA GLY PHE ALA THR ARG SEQRES 6 A 428 VAL ASP VAL LYS ILE HIS ALA ASP GLY SER VAL GLU VAL SEQRES 7 A 428 ARG ASP ASP GLY ARG GLY ILE PRO VAL GLU MET HIS ALA SEQRES 8 A 428 THR GLY MET PRO THR ILE ASP VAL VAL MET THR GLN LEU SEQRES 9 A 428 HIS ALA GLY GLY LYS PHE ASP GLY GLU THR TYR ALA VAL SEQRES 10 A 428 SER GLY GLY LEU HIS GLY VAL GLY VAL SER VAL VAL ASN SEQRES 11 A 428 ALA LEU SER THR ARG LEU GLU ALA THR VAL LEU ARG ASP SEQRES 12 A 428 GLY TYR GLU TRP PHE GLN TYR TYR ASP ARG SER VAL PRO SEQRES 13 A 428 GLY LYS LEU LYS GLN GLY GLY GLU THR LYS GLU THR GLY SEQRES 14 A 428 THR THR ILE ARG PHE TRP ALA ASP PRO GLU ILE PHE GLU SEQRES 15 A 428 THR THR ASP TYR ASN PHE GLU THR VAL ALA ARG ARG LEU SEQRES 16 A 428 GLN GLU MET ALA PHE LEU ASN LYS GLY LEU THR ILE GLU SEQRES 17 A 428 LEU THR ASP GLU ARG VAL THR ALA GLU GLU VAL VAL ASP SEQRES 18 A 428 ASP VAL VAL LYS ASP THR ALA GLU ALA PRO LYS THR ALA SEQRES 19 A 428 ASP GLU LYS ALA ALA GLU ALA THR GLY PRO SER LYS VAL SEQRES 20 A 428 LYS HIS ARG VAL PHE HIS TYR PRO GLY GLY LEU VAL ASP SEQRES 21 A 428 TYR VAL LYS HIS ILE ASN ARG THR LYS THR PRO ILE GLN SEQRES 22 A 428 GLN SER ILE ILE ASP PHE ASP GLY LYS GLY PRO GLY HIS SEQRES 23 A 428 GLU VAL GLU ILE ALA MET GLN TRP ASN ALA GLY TYR SER SEQRES 24 A 428 GLU SER VAL HIS THR PHE ALA ASN THR ILE ASN THR HIS SEQRES 25 A 428 GLU GLY GLY THR HIS GLU GLU GLY PHE ARG ALA ALA LEU SEQRES 26 A 428 THR SER VAL VAL ASN ARG TYR ALA LYS ASP LYS LYS LEU SEQRES 27 A 428 LEU LYS ASP LYS ASP PRO ASN LEU THR GLY ASP ASP ILE SEQRES 28 A 428 ARG GLU GLY LEU ALA ALA VAL ILE SER VAL LYS VAL ALA SEQRES 29 A 428 GLU PRO GLN PHE GLU GLY GLN THR LYS THR LYS LEU GLY SEQRES 30 A 428 ASN THR GLU VAL LYS SER PHE VAL GLN LYS ILE CYS ASN SEQRES 31 A 428 GLU GLN LEU GLN HIS TRP PHE GLU ALA ASN PRO ALA GLU SEQRES 32 A 428 ALA LYS THR VAL VAL ASN LYS ALA VAL SER SER ALA GLN SEQRES 33 A 428 ALA ARG ILE ALA ALA ARG LYS ALA ARG GLU LEU VAL HET ANP A 501 31 HET MG A 502 1 HET EDO A 503 4 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET NA A 508 1 HET NA A 509 1 HET NA A 510 1 HET K A 511 2 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETNAM K POTASSIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 EDO 5(C2 H6 O2) FORMUL 9 NA 3(NA 1+) FORMUL 12 K K 1+ FORMUL 13 HOH *296(H2 O) HELIX 1 AA1 GLY A 13 ILE A 17 5 5 HELIX 2 AA2 GLU A 21 ARG A 29 1 9 HELIX 3 AA3 ARG A 29 GLY A 35 1 7 HELIX 4 AA4 GLY A 38 ALA A 59 1 22 HELIX 5 AA5 PRO A 94 GLN A 102 1 9 HELIX 6 AA6 VAL A 123 LEU A 131 1 9 HELIX 7 AA7 ASN A 186 ASN A 201 1 16 HELIX 8 AA8 GLY A 255 ASN A 265 1 11 HELIX 9 AA9 ARG A 266 LYS A 268 5 3 HELIX 10 AB1 THR A 315 LYS A 335 1 21 HELIX 11 AB2 THR A 346 GLU A 352 1 7 HELIX 12 AB3 ASN A 377 ASN A 399 1 23 HELIX 13 AB4 ASN A 399 ALA A 423 1 25 SHEET 1 AA1 3 VAL A 154 PRO A 155 0 SHEET 2 AA1 3 TYR A 144 ASP A 151 -1 N ASP A 151 O VAL A 154 SHEET 3 AA1 3 LYS A 159 GLU A 163 -1 O GLY A 161 N GLU A 145 SHEET 1 AA2 8 VAL A 154 PRO A 155 0 SHEET 2 AA2 8 TYR A 144 ASP A 151 -1 N ASP A 151 O VAL A 154 SHEET 3 AA2 8 SER A 132 ARG A 141 -1 N ALA A 137 O GLN A 148 SHEET 4 AA2 8 GLY A 168 ALA A 175 -1 O ARG A 172 N GLU A 136 SHEET 5 AA2 8 VAL A 75 ASP A 79 -1 N VAL A 77 O ILE A 171 SHEET 6 AA2 8 ARG A 64 ILE A 69 -1 N ASP A 66 O ARG A 78 SHEET 7 AA2 8 THR A 205 ASP A 210 1 O GLU A 207 N VAL A 67 SHEET 8 AA2 8 HIS A 248 PHE A 251 -1 O PHE A 251 N ILE A 206 SHEET 1 AA3 5 ILE A 276 GLY A 282 0 SHEET 2 AA3 5 HIS A 285 TRP A 293 -1 O HIS A 285 N GLY A 282 SHEET 3 AA3 5 LEU A 354 VAL A 362 -1 O SER A 359 N GLU A 288 SHEET 4 AA3 5 SER A 300 ALA A 305 1 N SER A 300 O LEU A 354 SHEET 5 AA3 5 ILE A 308 ASN A 309 -1 O ILE A 308 N ALA A 305 SHEET 1 AA4 2 GLY A 313 GLY A 314 0 SHEET 2 AA4 2 LYS A 374 LEU A 375 1 O LEU A 375 N GLY A 313 LINK O LYS A 5 NA NA A 510 1555 1555 2.39 LINK O LYS A 5 NA NA A 510 1555 12535 2.39 LINK OD1 ASN A 7 NA NA A 510 1555 1555 2.40 LINK OD1 ASN A 7 NA NA A 510 1555 12535 2.40 LINK OD1 ASN A 52 MG MG A 502 1555 1555 2.05 LINK O ASP A 80 NA NA A 509 1555 1555 2.25 LINK O GLY A 81 NA NA A 509 1555 1555 2.35 LINK O VAL A 99 K A K A 511 1555 1555 2.93 LINK O VAL A 99 K B K A 511 1555 1555 2.49 LINK O GLN A 102 K B K A 511 1555 1555 2.08 LINK O ALA A 105 K A K A 511 1555 1555 2.77 LINK O LYS A 108 NA NA A 508 1555 1555 2.63 LINK O ASP A 110 NA NA A 508 1555 1555 2.52 LINK O GLY A 122 K A K A 511 1555 1555 2.92 LINK O GLY A 122 K B K A 511 1555 1555 2.95 LINK OG SER A 126 K A K A 511 1555 1555 3.48 LINK OG SER A 126 K B K A 511 1555 1555 2.38 LINK O THR A 167 NA NA A 509 1555 1555 2.58 LINK OG1 THR A 167 NA NA A 509 1555 1555 2.30 LINK O3G ANP A 501 MG MG A 502 1555 1555 2.08 LINK O2B ANP A 501 MG MG A 502 1555 1555 2.17 LINK O2A ANP A 501 MG MG A 502 1555 1555 2.20 LINK O1A ANP A 501 K A K A 511 1555 1555 2.77 LINK MG MG A 502 O HOH A 629 1555 1555 2.05 LINK MG MG A 502 O HOH A 705 1555 1555 2.20 LINK NA NA A 508 O HOH A 640 1555 1555 2.38 LINK NA NA A 508 O HOH A 648 1555 1555 2.49 LINK NA NA A 508 O HOH A 717 1555 1555 2.29 LINK NA NA A 508 O HOH A 855 1555 1555 2.56 LINK NA NA A 509 O HOH A 836 1555 1555 2.31 LINK NA NA A 509 O HOH A 847 1555 1555 2.36 LINK NA NA A 510 O HOH A 825 1555 1555 2.34 LINK NA NA A 510 O HOH A 825 1555 12535 2.34 SITE 1 AC1 30 TYR A 12 ILE A 17 GLU A 48 ASN A 52 SITE 2 AC1 30 GLU A 56 ASP A 79 ILE A 84 VAL A 99 SITE 3 AC1 30 GLY A 106 GLY A 107 LYS A 108 TYR A 114 SITE 4 AC1 30 GLY A 119 LEU A 120 HIS A 121 GLY A 122 SITE 5 AC1 30 VAL A 123 GLY A 124 VAL A 125 THR A 169 SITE 6 AC1 30 GLN A 370 LYS A 372 MG A 502 K A 511 SITE 7 AC1 30 HOH A 629 HOH A 658 HOH A 705 HOH A 706 SITE 8 AC1 30 HOH A 757 HOH A 758 SITE 1 AC2 4 ASN A 52 ANP A 501 HOH A 629 HOH A 705 SITE 1 AC3 6 GLU A 136 ALA A 137 THR A 138 ARG A 172 SITE 2 AC3 6 HOH A 701 HOH A 710 SITE 1 AC4 4 ASP A 66 LYS A 68 GLU A 76 ARG A 78 SITE 1 AC5 4 GLY A 284 GLU A 286 LYS A 361 HOH A 697 SITE 1 AC6 6 HIS A 44 TRP A 47 ARG A 193 HIS A 311 SITE 2 AC6 6 HOH A 603 HOH A 614 SITE 1 AC7 7 HIS A 44 GLU A 48 ASP A 51 GLN A 370 SITE 2 AC7 7 LYS A 372 HOH A 630 HOH A 767 SITE 1 AC8 6 LYS A 108 ASP A 110 HOH A 640 HOH A 648 SITE 2 AC8 6 HOH A 717 HOH A 855 SITE 1 AC9 5 ASP A 80 GLY A 81 THR A 167 HOH A 836 SITE 2 AC9 5 HOH A 847 SITE 1 AD1 3 LYS A 5 ASN A 7 HOH A 825 SITE 1 AD2 6 VAL A 99 GLN A 102 ALA A 105 GLY A 122 SITE 2 AD2 6 SER A 126 ANP A 501 CRYST1 76.985 76.985 261.476 90.00 90.00 120.00 P 61 2 2 12 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 0.012990 0.007500 0.000000 0.00000 SCALE2 0.000000 0.014999 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003824 0.00000