HEADER ISOMERASE 03-AUG-12 4GFJ TITLE CRYSTAL STRUCTURE OF TOPO-78, AN N-TERMINAL 78KDA FRAGMENT OF TITLE 2 TOPOISOMERASE V COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOPOISOMERASE V; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-685; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOPYRUS KANDLERI AV19; SOURCE 3 ORGANISM_TAXID: 190192; SOURCE 4 STRAIN: AV19; SOURCE 5 GENE: MK1436, TOPOISOMERASE V; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS HELIX-HAIRPIN-HELIX, DNA REPAIR ENZYME, TOPOISOMERASE, DNA BINDING, KEYWDS 2 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.RAJAN,R.PRASAD,B.TANEJA,S.H.WILSON,A.MONDRAGON REVDAT 3 13-SEP-23 4GFJ 1 REMARK REVDAT 2 09-JAN-13 4GFJ 1 JRNL REVDAT 1 05-DEC-12 4GFJ 0 JRNL AUTH R.RAJAN,R.PRASAD,B.TANEJA,S.H.WILSON,A.MONDRAGON JRNL TITL IDENTIFICATION OF ONE OF THE APURINIC/APYRIMIDINIC LYASE JRNL TITL 2 ACTIVE SITES OF TOPOISOMERASE V BY STRUCTURAL AND FUNCTIONAL JRNL TITL 3 STUDIES. JRNL REF NUCLEIC ACIDS RES. V. 41 657 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23125368 JRNL DOI 10.1093/NAR/GKS1017 REMARK 2 REMARK 2 RESOLUTION. 2.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 18292 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 989 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) : 2.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1263 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.21000 REMARK 3 B22 (A**2) : -2.21000 REMARK 3 B33 (A**2) : 3.32000 REMARK 3 B12 (A**2) : -1.11000 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): 0.413 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.312 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 35.583 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5057 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3650 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6805 ; 1.035 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8794 ; 0.817 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 613 ; 5.434 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;32.614 ;22.874 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 953 ;16.226 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 68 ;16.247 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 747 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5604 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1065 ; 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): 3045 ; 0.282 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1239 ; 0.039 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4903 ; 0.555 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2012 ; 1.086 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1902 ; 1.584 ; 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 : 6 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 3 A 217 REMARK 3 ORIGIN FOR THE GROUP (A): 33.9923 -55.6589 -3.1772 REMARK 3 T TENSOR REMARK 3 T11: 0.1704 T22: 0.2022 REMARK 3 T33: 0.1280 T12: 0.0249 REMARK 3 T13: -0.0365 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 3.6755 L22: 4.3271 REMARK 3 L33: 1.3098 L12: 0.5804 REMARK 3 L13: -0.2274 L23: 0.0834 REMARK 3 S TENSOR REMARK 3 S11: -0.0405 S12: 0.2137 S13: -0.1249 REMARK 3 S21: 0.0643 S22: 0.1065 S23: -0.0195 REMARK 3 S31: -0.0870 S32: -0.1363 S33: -0.0661 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 218 A 286 REMARK 3 ORIGIN FOR THE GROUP (A): 26.2595 -61.0863 -7.9220 REMARK 3 T TENSOR REMARK 3 T11: 0.1314 T22: 0.2277 REMARK 3 T33: 0.1309 T12: 0.0180 REMARK 3 T13: -0.0652 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 8.2094 L22: 1.9513 REMARK 3 L33: 1.2574 L12: 1.0872 REMARK 3 L13: -0.3681 L23: 0.5206 REMARK 3 S TENSOR REMARK 3 S11: -0.0846 S12: 0.6317 S13: -0.5315 REMARK 3 S21: -0.1430 S22: 0.0944 S23: 0.0081 REMARK 3 S31: -0.0845 S32: -0.1204 S33: -0.0098 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 287 A 358 REMARK 3 ORIGIN FOR THE GROUP (A): 33.3112 -48.8521 18.8336 REMARK 3 T TENSOR REMARK 3 T11: 0.4551 T22: 0.2334 REMARK 3 T33: 0.0653 T12: -0.2273 REMARK 3 T13: -0.0426 T23: 0.0906 REMARK 3 L TENSOR REMARK 3 L11: 16.5909 L22: 8.0455 REMARK 3 L33: 4.3401 L12: 8.6357 REMARK 3 L13: 0.6684 L23: -0.0739 REMARK 3 S TENSOR REMARK 3 S11: 0.7178 S12: -0.8679 S13: -0.1833 REMARK 3 S21: 0.8022 S22: -0.2921 S23: 0.1702 REMARK 3 S31: 0.0987 S32: -0.5027 S33: -0.4256 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 359 A 411 REMARK 3 ORIGIN FOR THE GROUP (A): 51.3363 -36.4201 7.1805 REMARK 3 T TENSOR REMARK 3 T11: 0.3107 T22: 0.1338 REMARK 3 T33: 0.2559 T12: -0.1218 REMARK 3 T13: -0.0862 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 5.7065 L22: 4.6775 REMARK 3 L33: 2.8978 L12: 2.1995 REMARK 3 L13: 0.7051 L23: 3.1041 REMARK 3 S TENSOR REMARK 3 S11: 0.3240 S12: -0.2211 S13: 0.0830 REMARK 3 S21: 0.1365 S22: -0.0696 S23: -0.2316 REMARK 3 S31: -0.0657 S32: 0.0972 S33: -0.2544 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 412 A 577 REMARK 3 ORIGIN FOR THE GROUP (A): 75.7633 -69.8223 -2.9358 REMARK 3 T TENSOR REMARK 3 T11: 0.1899 T22: 0.4195 REMARK 3 T33: 0.3667 T12: 0.0262 REMARK 3 T13: -0.1177 T23: -0.1769 REMARK 3 L TENSOR REMARK 3 L11: 2.6770 L22: 5.1961 REMARK 3 L33: 0.1998 L12: -2.4041 REMARK 3 L13: 0.7151 L23: -0.6781 REMARK 3 S TENSOR REMARK 3 S11: 0.2345 S12: 0.2316 S13: 0.1223 REMARK 3 S21: 0.1765 S22: -0.2078 S23: -0.2930 REMARK 3 S31: 0.0754 S32: 0.1016 S33: -0.0267 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 578 A 612 REMARK 3 ORIGIN FOR THE GROUP (A): 87.7556-107.7472 13.5425 REMARK 3 T TENSOR REMARK 3 T11: 0.4650 T22: 0.2168 REMARK 3 T33: 0.8520 T12: -0.1876 REMARK 3 T13: -0.2431 T23: 0.0172 REMARK 3 L TENSOR REMARK 3 L11: 5.0475 L22: 11.9514 REMARK 3 L33: 12.3448 L12: -2.3883 REMARK 3 L13: -0.3983 L23: -1.5711 REMARK 3 S TENSOR REMARK 3 S11: -0.5047 S12: 0.0697 S13: -0.9060 REMARK 3 S21: 0.7328 S22: 0.2663 S23: 0.3935 REMARK 3 S31: 0.8598 S32: -0.6304 S33: 0.2384 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 REMARK 4 REMARK 4 4GFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19283 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.910 REMARK 200 RESOLUTION RANGE LOW (A) : 29.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.56600 REMARK 200 R SYM FOR SHELL (I) : 0.51900 REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2CSB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES PH 7, 0.1 M KCL, 0.01 M REMARK 280 MGCL2, AND 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 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 19.40900 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 38.81800 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 29.11350 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 48.52250 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 9.70450 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: 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 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 1 REMARK 465 ALA A 2 REMARK 465 ALA A 613 REMARK 465 ALA A 614 REMARK 465 GLU A 615 REMARK 465 ILE A 616 REMARK 465 LYS A 617 REMARK 465 GLY A 618 REMARK 465 PRO A 619 REMARK 465 GLU A 620 REMARK 465 PHE A 621 REMARK 465 LYS A 622 REMARK 465 PHE A 623 REMARK 465 LEU A 624 REMARK 465 LEU A 625 REMARK 465 ASN A 626 REMARK 465 ILE A 627 REMARK 465 GLU A 628 REMARK 465 GLY A 629 REMARK 465 VAL A 630 REMARK 465 GLY A 631 REMARK 465 PRO A 632 REMARK 465 LYS A 633 REMARK 465 LEU A 634 REMARK 465 ALA A 635 REMARK 465 GLU A 636 REMARK 465 ARG A 637 REMARK 465 ILE A 638 REMARK 465 LEU A 639 REMARK 465 GLU A 640 REMARK 465 ALA A 641 REMARK 465 VAL A 642 REMARK 465 ASP A 643 REMARK 465 TYR A 644 REMARK 465 ASP A 645 REMARK 465 LEU A 646 REMARK 465 GLU A 647 REMARK 465 ARG A 648 REMARK 465 LEU A 649 REMARK 465 ALA A 650 REMARK 465 SER A 651 REMARK 465 LEU A 652 REMARK 465 ASN A 653 REMARK 465 PRO A 654 REMARK 465 GLU A 655 REMARK 465 GLU A 656 REMARK 465 LEU A 657 REMARK 465 ALA A 658 REMARK 465 GLU A 659 REMARK 465 LYS A 660 REMARK 465 VAL A 661 REMARK 465 GLU A 662 REMARK 465 GLY A 663 REMARK 465 LEU A 664 REMARK 465 GLY A 665 REMARK 465 GLU A 666 REMARK 465 GLU A 667 REMARK 465 LEU A 668 REMARK 465 ALA A 669 REMARK 465 GLU A 670 REMARK 465 ARG A 671 REMARK 465 VAL A 672 REMARK 465 VAL A 673 REMARK 465 TYR A 674 REMARK 465 ALA A 675 REMARK 465 ALA A 676 REMARK 465 ARG A 677 REMARK 465 GLU A 678 REMARK 465 ARG A 679 REMARK 465 VAL A 680 REMARK 465 GLU A 681 REMARK 465 SER A 682 REMARK 465 ARG A 683 REMARK 465 ARG A 684 REMARK 465 LYS A 685 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 ARG A 83 49.54 37.22 REMARK 500 VAL A 133 -81.23 -115.02 REMARK 500 ALA A 167 -109.57 -150.67 REMARK 500 ASN A 195 103.22 -163.32 REMARK 500 LYS A 282 -70.25 -21.29 REMARK 500 GLU A 375 -53.77 70.74 REMARK 500 SER A 451 15.66 -69.62 REMARK 500 LEU A 555 57.69 27.67 REMARK 500 PHE A 557 -146.31 -129.81 REMARK 500 ALA A 575 -68.08 -97.27 REMARK 500 SER A 590 -60.70 -106.63 REMARK 500 LEU A 591 -41.91 118.38 REMARK 500 ASP A 602 49.77 -70.10 REMARK 500 GLU A 605 -157.73 61.37 REMARK 500 ALA A 608 94.64 -69.98 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 ZN A 704 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 161 OE2 REMARK 620 2 GLU A 161 OE1 63.6 REMARK 620 3 HIS A 246 NE2 103.0 96.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M7G RELATED DB: PDB REMARK 900 STRUCTURE OF TOPOISOMERASE DOMAIN OF TOPOISOMERASE V PROTEIN REMARK 900 RELATED ID: 3M7D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE REMARK 900 V IN THE PRESENCE OF DIOXANE REMARK 900 RELATED ID: 3M6Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE REMARK 900 V IN THE PRESENCE OF GUANIDIUM HYDROCHLORIDE REMARK 900 RELATED ID: 3M6K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V REMARK 900 IN THE PRESENCE OF GUANIDIUM HYDROCHLORIDE REMARK 900 RELATED ID: 2CSB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TOPOISOMERASE V FROM METHANOPYRUS KANDLERI (61 REMARK 900 KDA FRAGMENT) REMARK 900 RELATED ID: 2CSD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TOPOISOMERASE V (61 KDA FRAGMENT) DBREF 4GFJ A 1 685 UNP F1SVL0 F1SVL0_METKA 1 685 SEQRES 1 A 685 MET ALA LEU VAL TYR ASP ALA GLU PHE VAL GLY SER GLU SEQRES 2 A 685 ARG GLU PHE GLU GLU GLU ARG GLU THR PHE LEU LYS GLY SEQRES 3 A 685 VAL LYS ALA TYR ASP GLY VAL LEU ALA THR ARG TYR LEU SEQRES 4 A 685 MET GLU ARG SER SER SER ALA LYS ASN ASP GLU GLU LEU SEQRES 5 A 685 LEU GLU LEU HIS GLN ASN PHE ILE LEU LEU THR GLY SER SEQRES 6 A 685 TYR ALA CYS SER ILE ASP PRO THR GLU ASP ARG TYR GLN SEQRES 7 A 685 ASN VAL ILE VAL ARG GLY VAL ASN PHE ASP GLU ARG VAL SEQRES 8 A 685 GLN ARG LEU SER THR GLY GLY SER PRO ALA ARG TYR ALA SEQRES 9 A 685 ILE VAL TYR ARG ARG GLY TRP ARG ALA ILE ALA LYS ALA SEQRES 10 A 685 LEU ASP ILE ASP GLU GLU ASP VAL PRO ALA ILE GLU VAL SEQRES 11 A 685 ARG ALA VAL LYS ARG ASN PRO LEU GLN PRO ALA LEU TYR SEQRES 12 A 685 ARG ILE LEU VAL ARG TYR GLY ARG VAL ASP LEU MET PRO SEQRES 13 A 685 VAL THR VAL ASP GLU VAL PRO PRO GLU MET ALA GLY GLU SEQRES 14 A 685 PHE GLU ARG LEU ILE GLU ARG TYR ASP VAL PRO ILE ASP SEQRES 15 A 685 GLU LYS GLU GLU ARG ILE LEU GLU ILE LEU ARG GLU ASN SEQRES 16 A 685 PRO TRP THR PRO HIS ASP GLU ILE ALA ARG ARG LEU GLY SEQRES 17 A 685 LEU SER VAL SER GLU VAL GLU GLY GLU LYS ASP PRO GLU SEQRES 18 A 685 SER SER GLY ILE TYR SER LEU TRP SER ARG VAL VAL VAL SEQRES 19 A 685 ASN ILE GLU TYR ASP GLU ARG THR ALA LYS ARG HIS VAL SEQRES 20 A 685 LYS ARG ARG ASP ARG LEU LEU GLU GLU LEU TYR GLU HIS SEQRES 21 A 685 LEU GLU GLU LEU SER GLU ARG TYR LEU ARG HIS PRO LEU SEQRES 22 A 685 THR ARG ARG TRP ILE VAL GLU HIS LYS ARG ASP ILE MET SEQRES 23 A 685 ARG ARG TYR LEU GLU GLN ARG ILE VAL GLU CYS ALA LEU SEQRES 24 A 685 LYS LEU GLN ASP ARG TYR GLY ILE ARG GLU ASP VAL ALA SEQRES 25 A 685 LEU CYS LEU ALA ARG ALA PHE ASP GLY SER ILE SER MET SEQRES 26 A 685 ILE ALA THR THR PRO TYR ARG THR LEU LYS ASP VAL CYS SEQRES 27 A 685 PRO ASP LEU THR LEU GLU GLU ALA LYS SER VAL ASN ARG SEQRES 28 A 685 THR LEU ALA THR LEU ILE ASP GLU HIS GLY LEU SER PRO SEQRES 29 A 685 ASP ALA ALA ASP GLU LEU ILE GLU HIS PHE GLU SER ILE SEQRES 30 A 685 ALA GLY ILE LEU ALA THR ASP LEU GLU GLU ILE GLU ARG SEQRES 31 A 685 MET TYR GLU GLU GLY ARG LEU SER GLU GLU ALA TYR ARG SEQRES 32 A 685 ALA ALA VAL GLU ILE GLN LEU ALA GLU LEU THR LYS LYS SEQRES 33 A 685 GLU GLY VAL GLY ARG LYS THR ALA GLU ARG LEU LEU ARG SEQRES 34 A 685 ALA PHE GLY ASN PRO GLU ARG VAL LYS GLN LEU ALA ARG SEQRES 35 A 685 GLU PHE GLU ILE GLU LYS LEU ALA SER VAL GLU GLY VAL SEQRES 36 A 685 GLY GLU ARG VAL LEU ARG SER LEU VAL PRO GLY TYR ALA SEQRES 37 A 685 SER LEU ILE SER ILE ARG GLY ILE ASP ARG GLU ARG ALA SEQRES 38 A 685 GLU ARG LEU LEU LYS LYS TYR GLY GLY TYR SER LYS VAL SEQRES 39 A 685 ARG GLU ALA GLY VAL GLU GLU LEU ARG GLU ASP GLY LEU SEQRES 40 A 685 THR ASP ALA GLN ILE ARG GLU LEU LYS GLY LEU LYS THR SEQRES 41 A 685 LEU GLU SER ILE VAL GLY ASP LEU GLU LYS ALA ASP GLU SEQRES 42 A 685 LEU LYS ARG LYS TYR GLY SER ALA SER ALA VAL ARG ARG SEQRES 43 A 685 LEU PRO VAL GLU GLU LEU ARG GLU LEU GLY PHE SER ASP SEQRES 44 A 685 ASP GLU ILE ALA GLU ILE LYS GLY ILE PRO LYS LYS LEU SEQRES 45 A 685 ARG GLU ALA PHE ASP LEU GLU THR ALA ALA GLU LEU TYR SEQRES 46 A 685 GLU ARG TYR GLY SER LEU LYS GLU ILE GLY ARG ARG LEU SEQRES 47 A 685 SER TYR ASP ASP LEU LEU GLU LEU GLY ALA THR PRO LYS SEQRES 48 A 685 ALA ALA ALA GLU ILE LYS GLY PRO GLU PHE LYS PHE LEU SEQRES 49 A 685 LEU ASN ILE GLU GLY VAL GLY PRO LYS LEU ALA GLU ARG SEQRES 50 A 685 ILE LEU GLU ALA VAL ASP TYR ASP LEU GLU ARG LEU ALA SEQRES 51 A 685 SER LEU ASN PRO GLU GLU LEU ALA GLU LYS VAL GLU GLY SEQRES 52 A 685 LEU GLY GLU GLU LEU ALA GLU ARG VAL VAL TYR ALA ALA SEQRES 53 A 685 ARG GLU ARG VAL GLU SER ARG ARG LYS HET GOL A 701 6 HET GOL A 702 6 HET GOL A 703 6 HET ZN A 704 1 HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *4(H2 O) HELIX 1 1 SER A 12 GLU A 41 1 30 HELIX 2 2 SER A 43 ASN A 48 1 6 HELIX 3 3 ASP A 49 SER A 69 1 21 HELIX 4 4 PHE A 87 LEU A 94 1 8 HELIX 5 5 SER A 99 VAL A 106 1 8 HELIX 6 6 GLY A 110 LEU A 118 1 9 HELIX 7 7 ASP A 121 VAL A 125 5 5 HELIX 8 8 GLN A 139 TYR A 149 1 11 HELIX 9 9 PRO A 163 ALA A 167 5 5 HELIX 10 10 PHE A 170 ARG A 176 1 7 HELIX 11 11 ASP A 182 ASN A 195 1 14 HELIX 12 12 PRO A 199 GLY A 208 1 10 HELIX 13 13 SER A 210 GLY A 216 1 7 HELIX 14 14 GLY A 224 ASN A 235 1 12 HELIX 15 15 ASP A 239 GLU A 266 1 28 HELIX 16 16 THR A 274 ARG A 304 1 31 HELIX 17 17 ARG A 308 PHE A 319 1 12 HELIX 18 18 SER A 322 THR A 328 1 7 HELIX 19 19 PRO A 330 CYS A 338 1 9 HELIX 20 20 THR A 342 ASN A 350 1 9 HELIX 21 21 ASN A 350 GLU A 359 1 10 HELIX 22 22 SER A 363 GLU A 375 1 13 HELIX 23 23 SER A 376 ALA A 382 1 7 HELIX 24 24 ASP A 384 GLU A 394 1 11 HELIX 25 25 SER A 398 LYS A 415 1 18 HELIX 26 26 GLY A 420 GLY A 432 1 13 HELIX 27 27 ASN A 433 GLU A 443 1 11 HELIX 28 28 GLU A 445 SER A 451 1 7 HELIX 29 29 GLY A 456 VAL A 464 1 9 HELIX 30 30 GLY A 466 SER A 472 1 7 HELIX 31 31 ASP A 477 GLY A 489 1 13 HELIX 32 32 GLY A 490 ALA A 497 1 8 HELIX 33 33 GLY A 498 ASP A 505 1 8 HELIX 34 34 THR A 508 GLY A 517 1 10 HELIX 35 35 LEU A 518 VAL A 525 1 8 HELIX 36 36 ASP A 527 TYR A 538 1 12 HELIX 37 37 SER A 540 LEU A 547 1 8 HELIX 38 38 PRO A 548 GLU A 554 1 7 HELIX 39 39 SER A 558 GLY A 567 1 10 HELIX 40 40 PRO A 569 PHE A 576 1 8 HELIX 41 41 ASP A 577 GLY A 589 1 13 HELIX 42 42 LYS A 592 ARG A 597 5 6 HELIX 43 43 LEU A 598 ASP A 602 5 5 HELIX 44 44 ALA A 608 ALA A 612 5 5 SHEET 1 A 3 ASP A 6 PHE A 9 0 SHEET 2 A 3 TYR A 77 VAL A 82 -1 O ILE A 81 N ASP A 6 SHEET 3 A 3 VAL A 85 ASN A 86 -1 O VAL A 85 N VAL A 82 SSBOND 1 CYS A 314 CYS A 338 1555 1555 2.04 LINK OE2 GLU A 161 ZN ZN A 704 1555 1555 2.05 LINK OE1 GLU A 161 ZN ZN A 704 1555 1555 2.06 LINK NE2 HIS A 246 ZN ZN A 704 1555 1555 2.16 SITE 1 AC1 3 VAL A 133 LYS A 134 GOL A 703 SITE 1 AC2 4 GLU A 221 ASP A 384 PHE A 431 GLY A 432 SITE 1 AC3 6 ARG A 108 ARG A 131 VAL A 133 ARG A 293 SITE 2 AC3 6 SER A 322 GOL A 701 SITE 1 AC4 3 GLU A 161 GLU A 194 HIS A 246 CRYST1 161.634 161.634 58.227 90.00 90.00 120.00 P 61 6 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 0.006187 0.003572 0.000000 0.00000 SCALE2 0.000000 0.007144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017174 0.00000