PDB Short entry for 1Z59 HEADER ISOMERASE 17-MAR-05 1Z59 TITLE TOPOISOMERASE VI-B, ADP-BOUND MONOMER FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE II DNA TOPOISOMERASE VI SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TOPOVI-B; COMPND 5 EC: 5.99.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SHIBATAE; SOURCE 3 ORGANISM_TAXID: 2286; SOURCE 4 GENE: TOP6B; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS TOPOISOMERASE, ARCHAEA, ATPASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.D.CORBETT,J.M.BERGER REVDAT 5 15-NOV-23 1Z59 1 REMARK REVDAT 4 23-AUG-23 1Z59 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1Z59 1 VERSN REVDAT 2 24-FEB-09 1Z59 1 VERSN REVDAT 1 14-JUN-05 1Z59 0 JRNL AUTH K.D.CORBETT,J.M.BERGER JRNL TITL STRUCTURAL DISSECTION OF ATP TURNOVER IN THE PROTOTYPICAL JRNL TITL 2 GHL ATPASE TOPOVI. JRNL REF STRUCTURE V. 13 873 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 15939019 JRNL DOI 10.1016/J.STR.2005.03.013 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 32440 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2916 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2384 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 200 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3696 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.88000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 1.87000 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): 0.171 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3804 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5155 ; 1.171 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 461 ; 6.355 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 573 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2833 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1439 ; 0.199 ; 0.200 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): 126 ; 0.139 ; 0.200 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): 37 ; 0.239 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.059 ; 0.200 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): 2314 ; 0.704 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3775 ; 1.339 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1490 ; 2.657 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1380 ; 4.338 ; 4.500 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 229 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7380 56.2150 10.1228 REMARK 3 T TENSOR REMARK 3 T11: 0.1784 T22: 0.1842 REMARK 3 T33: 0.1503 T12: 0.0020 REMARK 3 T13: 0.0085 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.4719 L22: 0.8388 REMARK 3 L33: 0.1696 L12: 0.0705 REMARK 3 L13: 0.0415 L23: 0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.0374 S12: -0.0086 S13: 0.0239 REMARK 3 S21: 0.0334 S22: -0.0321 S23: -0.0463 REMARK 3 S31: -0.0207 S32: 0.0116 S33: -0.0052 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 230 A 310 REMARK 3 ORIGIN FOR THE GROUP (A): 37.0370 34.6646 34.6571 REMARK 3 T TENSOR REMARK 3 T11: 0.1438 T22: 0.0736 REMARK 3 T33: 0.0859 T12: -0.0183 REMARK 3 T13: -0.0928 T23: 0.0430 REMARK 3 L TENSOR REMARK 3 L11: 3.3111 L22: 2.2955 REMARK 3 L33: 4.8148 L12: 0.2709 REMARK 3 L13: 2.4909 L23: 0.1640 REMARK 3 S TENSOR REMARK 3 S11: -0.3742 S12: 0.0059 S13: 0.1999 REMARK 3 S21: 0.0970 S22: 0.0613 S23: -0.0550 REMARK 3 S31: -0.2174 S32: 0.1657 S33: 0.3129 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 311 A 470 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1052 27.9019 2.9086 REMARK 3 T TENSOR REMARK 3 T11: 0.1713 T22: 0.1795 REMARK 3 T33: 0.1929 T12: 0.0206 REMARK 3 T13: 0.0058 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 0.8683 L22: 0.9619 REMARK 3 L33: 0.1687 L12: 0.7323 REMARK 3 L13: 0.4173 L23: 0.3687 REMARK 3 S TENSOR REMARK 3 S11: -0.0008 S12: 0.0587 S13: -0.0844 REMARK 3 S21: -0.0045 S22: -0.0014 S23: -0.0548 REMARK 3 S31: 0.0188 S32: -0.0061 S33: 0.0022 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Z59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35386 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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: PDB ENTRY 1MU5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, NACL, MG(HCO2)2, PEG-3350, REMARK 280 MGCL2, ADP, PH 7.5, MICROBATCH, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 47.28650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.22550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.28650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.22550 REMARK 290 SMTRY3 4 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 300 REMARK: THE BIOLOGICAL UNIT IS THE MONOMER CONTAINED IN THE REMARK 300 ASYMMETRIC UNIT 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 4 REMARK 465 GLU A 5 REMARK 465 LYS A 6 REMARK 465 PHE A 7 REMARK 465 THR A 8 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 SER A 9 OG REMARK 470 TYR A 95 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 ARG A 250 CG CD NE CZ NH1 NH2 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 NH2 ARG A 238 OG1 THR A 294 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MSE A 107 SE MSE A 107 CE -0.750 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 382 CB - CG - OD2 ANGL. DEV. = 5.5 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 THR A 47 -73.52 -110.79 REMARK 500 LYS A 343 -165.18 -115.41 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 A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 42 OD1 REMARK 620 2 ADP A2001 O1B 88.2 REMARK 620 3 ADP A2001 O2A 95.4 82.4 REMARK 620 4 HOH A2015 O 91.3 168.6 86.3 REMARK 620 5 HOH A2059 O 171.8 88.0 91.3 93.9 REMARK 620 6 HOH A2084 O 83.9 102.4 175.1 88.9 89.8 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 MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MU5 RELATED DB: PDB REMARK 900 TOPOISOMERASE VI-B, APO MONOMER FORM REMARK 900 RELATED ID: 1MX0 RELATED DB: PDB REMARK 900 TOPOISOMERASE VI-B, AMPPNP-BOUND DIMER FORM REMARK 900 RELATED ID: 1Z5A RELATED DB: PDB REMARK 900 TOPOISOMERASE VI-B, ADP-BOUND DIMER FORM REMARK 900 RELATED ID: 1Z5B RELATED DB: PDB REMARK 900 TOPOISOMERASE VI-B, ADP ALF4- BOUND DIMER FORM REMARK 900 RELATED ID: 1Z5C RELATED DB: PDB REMARK 900 TOPOISOMERASE VI-B, ADP PI BOUND DIMER FORM REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN SEQUENCE DIFFERS FROM THE STANDARD REFERENCE REMARK 999 BECAUSE OF AN ERROR IN THE INITIALLY REPORTED SEQUENCE. REMARK 999 THE SEQUENCE OF THIS ENTRY IS BELIEVED TO BE CORRECT. DBREF 1Z59 A 2 470 UNP O05207 TOP6B_SULSH 2 470 SEQADV 1Z59 MSE A 107 UNP O05207 MET 107 MODIFIED RESIDUE SEQADV 1Z59 MSE A 121 UNP O05207 MET 121 MODIFIED RESIDUE SEQADV 1Z59 TYR A 303 UNP O05207 ASP 303 SEE REMARK 999 SEQADV 1Z59 MSE A 409 UNP O05207 MET 409 MODIFIED RESIDUE SEQADV 1Z59 MSE A 412 UNP O05207 MET 412 MODIFIED RESIDUE SEQADV 1Z59 ASP A 435 UNP O05207 ASN 435 SEE REMARK 999 SEQADV 1Z59 MSE A 445 UNP O05207 MET 445 MODIFIED RESIDUE SEQRES 1 A 469 SER ALA LYS GLU LYS PHE THR SER LEU SER PRO ALA GLU SEQRES 2 A 469 PHE PHE LYS ARG ASN PRO GLU LEU ALA GLY PHE PRO ASN SEQRES 3 A 469 PRO ALA ARG ALA LEU TYR GLN THR VAL ARG GLU LEU ILE SEQRES 4 A 469 GLU ASN SER LEU ASP ALA THR ASP VAL HIS GLY ILE LEU SEQRES 5 A 469 PRO ASN ILE LYS ILE THR ILE ASP LEU ILE ASP ASP ALA SEQRES 6 A 469 ARG GLN ILE TYR LYS VAL ASN VAL VAL ASP ASN GLY ILE SEQRES 7 A 469 GLY ILE PRO PRO GLN GLU VAL PRO ASN ALA PHE GLY ARG SEQRES 8 A 469 VAL LEU TYR SER SER LYS TYR VAL ASN ARG GLN THR ARG SEQRES 9 A 469 GLY MSE TYR GLY LEU GLY VAL LYS ALA ALA VAL LEU TYR SEQRES 10 A 469 SER GLN MSE HIS GLN ASP LYS PRO ILE GLU ILE GLU THR SEQRES 11 A 469 SER PRO VAL ASN SER LYS ARG ILE TYR THR PHE LYS LEU SEQRES 12 A 469 LYS ILE ASP ILE ASN LYS ASN GLU PRO ILE ILE VAL GLU SEQRES 13 A 469 ARG GLY SER VAL GLU ASN THR ARG GLY PHE HIS GLY THR SEQRES 14 A 469 SER VAL ALA ILE SER ILE PRO GLY ASP TRP PRO LYS ALA SEQRES 15 A 469 LYS SER ARG ILE TYR GLU TYR ILE LYS ARG THR TYR ILE SEQRES 16 A 469 ILE THR PRO TYR ALA GLU PHE ILE PHE LYS ASP PRO GLU SEQRES 17 A 469 GLY ASN VAL THR TYR TYR PRO ARG LEU THR ASN LYS ILE SEQRES 18 A 469 PRO LYS PRO PRO GLN GLU VAL LYS PRO HIS PRO TYR GLY SEQRES 19 A 469 VAL ASP ARG GLU GLU ILE LYS ILE LEU ILE ASN ASN LEU SEQRES 20 A 469 LYS ARG ASP TYR THR ILE LYS GLU PHE LEU VAL ASN GLU SEQRES 21 A 469 PHE GLN SER ILE GLY ASP THR THR ALA ASP LYS ILE LEU SEQRES 22 A 469 GLU LEU ALA GLY LEU LYS PRO ASN LYS LYS VAL LYS ASN SEQRES 23 A 469 LEU THR GLU GLU GLU ILE THR ARG LEU VAL GLU THR PHE SEQRES 24 A 469 LYS LYS TYR GLU ASP PHE ARG SER PRO SER ALA ASP SER SEQRES 25 A 469 LEU SER VAL ILE GLY GLU ASP LEU ILE GLU LEU GLY LEU SEQRES 26 A 469 LYS LYS ILE PHE ASN PRO ASP PHE ALA ALA SER ILE THR SEQRES 27 A 469 ARG LYS PRO LYS ALA TYR GLN GLY HIS PRO PHE ILE VAL SEQRES 28 A 469 GLU ALA GLY VAL ALA PHE GLY GLY SER ILE PRO VAL GLY SEQRES 29 A 469 GLU GLU PRO ILE VAL LEU ARG TYR ALA ASN LYS ILE PRO SEQRES 30 A 469 LEU ILE TYR ASP GLU LYS SER ASP VAL ILE TRP LYS VAL SEQRES 31 A 469 VAL GLU GLU LEU ASP TRP LYS ARG TYR GLY ILE GLU SER SEQRES 32 A 469 ASP GLN TYR GLN MSE VAL VAL MSE VAL HIS LEU CYS SER SEQRES 33 A 469 THR LYS ILE PRO TYR LYS SER ALA GLY LYS GLU SER ILE SEQRES 34 A 469 ALA GLU VAL GLU ASP ILE GLU LYS GLU ILE LYS ASN ALA SEQRES 35 A 469 LEU MSE GLU VAL ALA ARG LYS LEU LYS GLN TYR LEU SER SEQRES 36 A 469 GLU LYS ARG LYS GLU GLN GLU ALA LYS LYS LYS LEU LEU SEQRES 37 A 469 ALA MODRES 1Z59 MSE A 107 MET SELENOMETHIONINE MODRES 1Z59 MSE A 121 MET SELENOMETHIONINE MODRES 1Z59 MSE A 409 MET SELENOMETHIONINE MODRES 1Z59 MSE A 412 MET SELENOMETHIONINE MODRES 1Z59 MSE A 445 MET SELENOMETHIONINE HET MSE A 107 8 HET MSE A 121 8 HET MSE A 409 8 HET MSE A 412 8 HET MSE A 445 8 HET MG A1001 1 HET ADP A2001 27 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 MG MG 2+ FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 HOH *170(H2 O) HELIX 1 1 SER A 11 ASN A 19 1 9 HELIX 2 2 PRO A 20 ALA A 23 5 4 HELIX 3 3 ASN A 27 ALA A 46 1 20 HELIX 4 4 THR A 47 GLY A 51 5 5 HELIX 5 5 PRO A 82 GLN A 84 5 3 HELIX 6 6 GLU A 85 ARG A 92 1 8 HELIX 7 7 GLY A 111 GLN A 123 1 13 HELIX 8 8 ASP A 179 THR A 198 1 20 HELIX 9 9 HIS A 232 VAL A 236 5 5 HELIX 10 10 ASP A 237 LEU A 248 1 12 HELIX 11 11 THR A 253 PHE A 262 1 10 HELIX 12 12 GLY A 266 GLY A 278 1 13 HELIX 13 13 LYS A 284 LEU A 288 5 5 HELIX 14 14 THR A 289 TYR A 303 1 15 HELIX 15 15 SER A 310 LEU A 314 5 5 HELIX 16 16 GLY A 318 ASN A 331 1 14 HELIX 17 17 ASP A 382 SER A 385 5 4 HELIX 18 18 ASP A 386 LEU A 395 1 10 HELIX 19 19 ASP A 396 GLY A 401 5 6 HELIX 20 20 VAL A 433 LEU A 469 1 37 SHEET 1 A 8 PRO A 153 GLU A 162 0 SHEET 2 A 8 ARG A 138 ILE A 146 -1 N LYS A 145 O ILE A 154 SHEET 3 A 8 ILE A 127 SER A 132 -1 N THR A 131 O TYR A 140 SHEET 4 A 8 GLY A 169 PRO A 177 -1 O SER A 171 N GLU A 130 SHEET 5 A 8 ILE A 69 VAL A 75 -1 N TYR A 70 O ILE A 176 SHEET 6 A 8 ASN A 55 ASP A 64 -1 N THR A 59 O ASN A 73 SHEET 7 A 8 GLU A 202 LYS A 206 1 O ILE A 204 N ILE A 58 SHEET 8 A 8 VAL A 212 TYR A 215 -1 O TYR A 215 N PHE A 203 SHEET 1 B 3 PHE A 334 THR A 339 0 SHEET 2 B 3 HIS A 348 PHE A 358 -1 O PHE A 358 N PHE A 334 SHEET 3 B 3 LYS A 343 TYR A 345 -1 N LYS A 343 O PHE A 350 SHEET 1 C 5 PHE A 334 THR A 339 0 SHEET 2 C 5 HIS A 348 PHE A 358 -1 O PHE A 358 N PHE A 334 SHEET 3 C 5 MSE A 409 SER A 417 -1 O HIS A 414 N GLU A 353 SHEET 4 C 5 ILE A 369 ALA A 374 1 N ILE A 369 O VAL A 411 SHEET 5 C 5 ILE A 377 LEU A 379 -1 O LEU A 379 N ARG A 372 LINK C GLY A 106 N MSE A 107 1555 1555 1.34 LINK C MSE A 107 N TYR A 108 1555 1555 1.35 LINK C GLN A 120 N MSE A 121 1555 1555 1.34 LINK C MSE A 121 N HIS A 122 1555 1555 1.33 LINK C GLN A 408 N MSE A 409 1555 1555 1.34 LINK C MSE A 409 N VAL A 410 1555 1555 1.34 LINK C VAL A 411 N MSE A 412 1555 1555 1.34 LINK C MSE A 412 N VAL A 413 1555 1555 1.34 LINK C LEU A 444 N MSE A 445 1555 1555 1.32 LINK C MSE A 445 N GLU A 446 1555 1555 1.33 LINK OD1 ASN A 42 MG MG A1001 1555 1555 2.08 LINK MG MG A1001 O1B ADP A2001 1555 1555 2.12 LINK MG MG A1001 O2A ADP A2001 1555 1555 2.14 LINK MG MG A1001 O HOH A2015 1555 1555 2.25 LINK MG MG A1001 O HOH A2059 1555 1555 2.18 LINK MG MG A1001 O HOH A2084 1555 1555 2.12 SITE 1 AC1 5 ASN A 42 ADP A2001 HOH A2015 HOH A2059 SITE 2 AC1 5 HOH A2084 SITE 1 AC2 17 ASN A 42 ALA A 46 ASP A 76 GLY A 80 SITE 2 AC2 17 ILE A 81 ALA A 89 LEU A 110 VAL A 112 SITE 3 AC2 17 LYS A 113 THR A 170 MG A1001 HOH A2006 SITE 4 AC2 17 HOH A2013 HOH A2015 HOH A2059 HOH A2069 SITE 5 AC2 17 HOH A2112 CRYST1 94.573 112.451 56.079 90.00 90.00 90.00 P 21 21 2 4 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 0.010574 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017832 0.00000