HEADER ISOMERASE 16-MAR-10 3M7D TITLE CRYSTAL STRUCTURE OF AN N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V TITLE 2 IN THE PRESENCE OF DIOXANE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOPOISOMERASE V; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL 44 KDA FRAGMENT (TOPO-44); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOPYRUS KANDLERI; SOURCE 3 ORGANISM_TAXID: 190192; SOURCE 4 STRAIN: AV19; SOURCE 5 GENE: MK1436, TOP5, TOPOISOMERASE V; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HELIX-HAIRPIN-HELIX, TOPOISOMERASE, CONFORMATIONAL CHANGE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.RAJAN,B.TANEJA,A.MONDRAGON REVDAT 2 06-SEP-23 3M7D 1 REMARK REVDAT 1 04-AUG-10 3M7D 0 JRNL AUTH R.RAJAN,B.TANEJA,A.MONDRAGON JRNL TITL STRUCTURES OF MINIMAL CATALYTIC FRAGMENTS OF TOPOISOMERASE V JRNL TITL 2 REVEALS CONFORMATIONAL CHANGES RELEVANT FOR DNA BINDING. JRNL REF STRUCTURE V. 18 829 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20637419 JRNL DOI 10.1016/J.STR.2010.03.006 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 31317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1673 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.0591 - 4.1515 1.00 2722 169 0.1555 0.1937 REMARK 3 2 4.1515 - 3.2968 1.00 2688 130 0.1540 0.1984 REMARK 3 3 3.2968 - 2.8806 1.00 2666 145 0.1846 0.2078 REMARK 3 4 2.8806 - 2.6174 1.00 2616 163 0.1916 0.2386 REMARK 3 5 2.6174 - 2.4299 1.00 2700 133 0.1758 0.2087 REMARK 3 6 2.4299 - 2.2867 1.00 2606 139 0.1739 0.2273 REMARK 3 7 2.2867 - 2.1722 1.00 2680 118 0.1786 0.2383 REMARK 3 8 2.1722 - 2.0777 1.00 2630 140 0.1734 0.2179 REMARK 3 9 2.0777 - 1.9977 1.00 2649 142 0.1782 0.2546 REMARK 3 10 1.9977 - 1.9288 1.00 2636 132 0.1922 0.2575 REMARK 3 11 1.9288 - 1.8685 0.98 2596 143 0.1990 0.2798 REMARK 3 12 1.8685 - 1.8150 0.82 2128 119 0.1786 0.2481 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 29.69 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.63950 REMARK 3 B22 (A**2) : 0.87950 REMARK 3 B33 (A**2) : 3.76000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.42130 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3279 REMARK 3 ANGLE : 0.920 4454 REMARK 3 CHIRALITY : 0.065 486 REMARK 3 PLANARITY : 0.004 595 REMARK 3 DIHEDRAL : 16.074 1279 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 15.7542 20.1689 22.4720 REMARK 3 T TENSOR REMARK 3 T11: 0.0550 T22: 0.0620 REMARK 3 T33: 0.0553 T12: 0.0064 REMARK 3 T13: -0.0033 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.3283 L22: 0.4627 REMARK 3 L33: 0.3221 L12: -0.0740 REMARK 3 L13: 0.0386 L23: -0.1703 REMARK 3 S TENSOR REMARK 3 S11: 0.0451 S12: -0.0103 S13: -0.0143 REMARK 3 S21: -0.0329 S22: -0.0119 S23: 0.0741 REMARK 3 S31: 0.0126 S32: -0.0062 S33: -0.0279 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3M7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 78 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96500 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32998 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.815 REMARK 200 RESOLUTION RANGE LOW (A) : 75.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.19400 REMARK 200 R SYM FOR SHELL (I) : 0.16300 REMARK 200 FOR SHELL : 6.800 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: N-TERMINAL 31 KDA TOPOISOMERASE DOMAIN OF TOPO-61 REMARK 200 (2CSB) STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PHOSPATE CITRATE PH 5, 0.2 M REMARK 280 NACL, 15% PEG 3350, 8% DIOXANE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 52.07500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.07500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.87000 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 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 LEU A 3 REMARK 465 ASN A 48 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 ASP A 75 17.01 -153.82 REMARK 500 VAL A 125 71.03 40.89 REMARK 500 VAL A 133 -77.29 -114.64 REMARK 500 ALA A 167 -109.01 -140.92 REMARK 500 ALA A 167 -109.01 -142.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M6K RELATED DB: PDB REMARK 900 STRUCTURE OF THE 44 KDA N-TERMINAL FRAGMENT OF TOPOISOMERASE V WITH REMARK 900 GUANIDIUM HYDROCHLORIDE IN A DIFFERENT CRYSTALLIZATION CONDITION REMARK 900 RELATED ID: 3M6Z RELATED DB: PDB REMARK 900 STRUCTURE OF THE N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V IN REMARK 900 THE PRESENCE OF GUANIDIUM HYDROCHLORIDE REMARK 900 RELATED ID: 3M7G RELATED DB: PDB DBREF 3M7D A 1 380 UNP Q977W1 Q977W1_METKA 1 380 SEQRES 1 A 380 MET ALA LEU VAL TYR ASP ALA GLU PHE VAL GLY SER GLU SEQRES 2 A 380 ARG GLU PHE GLU GLU GLU ARG GLU THR PHE LEU LYS GLY SEQRES 3 A 380 VAL LYS ALA TYR ASP GLY VAL LEU ALA THR ARG TYR LEU SEQRES 4 A 380 MET GLU ARG SER SER SER ALA LYS ASN ASP GLU GLU LEU SEQRES 5 A 380 LEU GLU LEU HIS GLN ASN PHE ILE LEU LEU THR GLY SER SEQRES 6 A 380 TYR ALA CYS SER ILE ASP PRO THR GLU ASP ARG TYR GLN SEQRES 7 A 380 ASN VAL ILE VAL ARG GLY VAL ASN PHE ASP GLU ARG VAL SEQRES 8 A 380 GLN ARG LEU SER THR GLY GLY SER PRO ALA ARG TYR ALA SEQRES 9 A 380 ILE VAL TYR ARG ARG GLY TRP ARG ALA ILE ALA LYS ALA SEQRES 10 A 380 LEU ASP ILE ASP GLU GLU ASP VAL PRO ALA ILE GLU VAL SEQRES 11 A 380 ARG ALA VAL LYS ARG ASN PRO LEU GLN PRO ALA LEU TYR SEQRES 12 A 380 ARG ILE LEU VAL ARG TYR GLY ARG VAL ASP LEU MET PRO SEQRES 13 A 380 VAL THR VAL ASP GLU VAL PRO PRO GLU MET ALA GLY GLU SEQRES 14 A 380 PHE GLU ARG LEU ILE GLU ARG TYR ASP VAL PRO ILE ASP SEQRES 15 A 380 GLU LYS GLU GLU ARG ILE LEU GLU ILE LEU ARG GLU ASN SEQRES 16 A 380 PRO TRP THR PRO HIS ASP GLU ILE ALA ARG ARG LEU GLY SEQRES 17 A 380 LEU SER VAL SER GLU VAL GLU GLY GLU LYS ASP PRO GLU SEQRES 18 A 380 SER SER GLY ILE TYR SER LEU TRP SER ARG VAL VAL VAL SEQRES 19 A 380 ASN ILE GLU TYR ASP GLU ARG THR ALA LYS ARG HIS VAL SEQRES 20 A 380 LYS ARG ARG ASP ARG LEU LEU GLU GLU LEU TYR GLU HIS SEQRES 21 A 380 LEU GLU GLU LEU SER GLU ARG TYR LEU ARG HIS PRO LEU SEQRES 22 A 380 THR ARG ARG TRP ILE VAL GLU HIS LYS ARG ASP ILE MET SEQRES 23 A 380 ARG ARG TYR LEU GLU GLN ARG ILE VAL GLU CYS ALA LEU SEQRES 24 A 380 LYS LEU GLN ASP ARG TYR GLY ILE ARG GLU ASP VAL ALA SEQRES 25 A 380 LEU CYS LEU ALA ARG ALA PHE ASP GLY SER ILE SER MET SEQRES 26 A 380 ILE ALA THR THR PRO TYR ARG THR LEU LYS ASP VAL CYS SEQRES 27 A 380 PRO ASP LEU THR LEU GLU GLU ALA LYS SER VAL ASN ARG SEQRES 28 A 380 THR LEU ALA THR LEU ILE ASP GLU HIS GLY LEU SER PRO SEQRES 29 A 380 ASP ALA ALA ASP GLU LEU ILE GLU HIS PHE GLU SER ILE SEQRES 30 A 380 ALA GLY ILE FORMUL 2 HOH *238(H2 O) HELIX 1 1 SER A 12 SER A 43 1 32 HELIX 2 2 ASP A 49 SER A 69 1 21 HELIX 3 3 PHE A 87 ARG A 93 1 7 HELIX 4 4 SER A 99 VAL A 106 1 8 HELIX 5 5 GLY A 110 LEU A 118 1 9 HELIX 6 6 GLN A 139 TYR A 149 1 11 HELIX 7 7 THR A 158 VAL A 162 5 5 HELIX 8 8 PRO A 163 ALA A 167 5 5 HELIX 9 9 GLU A 169 TYR A 177 1 9 HELIX 10 10 ASP A 182 ASN A 195 1 14 HELIX 11 11 PRO A 199 GLY A 208 1 10 HELIX 12 12 SER A 210 GLY A 216 1 7 HELIX 13 13 GLY A 224 VAL A 234 1 11 HELIX 14 14 ASP A 239 GLU A 266 1 28 HELIX 15 15 THR A 274 HIS A 281 1 8 HELIX 16 16 HIS A 281 ARG A 304 1 24 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 SHEET 1 A 3 TYR A 5 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 2.05 CRYST1 104.150 47.740 81.223 90.00 112.48 90.00 C 1 2 1 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 0.009602 0.000000 0.003974 0.00000 SCALE2 0.000000 0.020947 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013324 0.00000