HEADER ISOMERASE 16-MAR-10 3M6Z TITLE CRYSTAL STRUCTURE OF AN N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V TITLE 2 IN THE PRESENCE OF GUANIDIUM HYDROCHLORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOPOISOMERASE V; COMPND 3 CHAIN: A, B; 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_VECTOR: PET15B KEYWDS HELIX-HAIRPIN-HELIX, TOPOISOMERASE, CONFORMATIONAL CHANGES IN KEYWDS 2 PROTEIN, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.RAJAN,B.TANEJA,A.MONDRAGON REVDAT 1 04-AUG-10 3M6Z 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. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 129802 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6859 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8967 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 487 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6056 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 573 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52000 REMARK 3 B22 (A**2) : -0.32000 REMARK 3 B33 (A**2) : -0.20000 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): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.897 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7757 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 5612 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10603 ; 1.195 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13490 ; 0.901 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 990 ; 4.709 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 440 ;32.878 ;22.409 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1456 ;12.794 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 127 ;18.476 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1095 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9168 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1806 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1814 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 6329 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3777 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 4075 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 485 ; 0.138 ; 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): 51 ; 0.266 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 163 ; 0.242 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 67 ; 0.146 ; 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): 6134 ; 0.778 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1794 ; 0.175 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7544 ; 0.892 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3593 ; 1.651 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3059 ; 2.181 ; 4.500 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : B A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 4 B 280 4 REMARK 3 1 A 4 A 280 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 B (A): 3299 ; 0.58 ; 0.50 REMARK 3 MEDIUM THERMAL 1 B (A**2): 3299 ; 0.93 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 281 B 374 4 REMARK 3 1 A 281 A 374 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 B (A): 1004 ; 0.72 ; 0.50 REMARK 3 MEDIUM THERMAL 2 B (A**2): 1004 ; 0.91 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 4 A 280 REMARK 3 ORIGIN FOR THE GROUP (A): 33.4230 54.4630 30.6550 REMARK 3 T TENSOR REMARK 3 T11: -0.0158 T22: -0.0365 REMARK 3 T33: -0.0242 T12: -0.0075 REMARK 3 T13: 0.0025 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.3087 L22: 0.5497 REMARK 3 L33: 0.2242 L12: -0.0484 REMARK 3 L13: 0.1407 L23: 0.1250 REMARK 3 S TENSOR REMARK 3 S11: -0.0093 S12: -0.0019 S13: 0.0150 REMARK 3 S21: -0.0766 S22: 0.0058 S23: -0.0037 REMARK 3 S31: -0.0181 S32: -0.0147 S33: 0.0035 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 281 A 378 REMARK 3 ORIGIN FOR THE GROUP (A): 51.7240 43.3160 25.4160 REMARK 3 T TENSOR REMARK 3 T11: -0.0595 T22: 0.0073 REMARK 3 T33: -0.0403 T12: -0.0052 REMARK 3 T13: 0.0039 T23: -0.0215 REMARK 3 L TENSOR REMARK 3 L11: 0.4794 L22: 0.6989 REMARK 3 L33: 1.5916 L12: 0.0126 REMARK 3 L13: 0.2897 L23: 0.5390 REMARK 3 S TENSOR REMARK 3 S11: 0.0279 S12: 0.1403 S13: -0.0148 REMARK 3 S21: -0.0609 S22: 0.0764 S23: -0.0735 REMARK 3 S31: -0.0289 S32: 0.2435 S33: -0.1042 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 : B 4 B 280 REMARK 3 ORIGIN FOR THE GROUP (A): 56.6540 86.9210 11.2670 REMARK 3 T TENSOR REMARK 3 T11: -0.0282 T22: -0.0137 REMARK 3 T33: -0.0194 T12: -0.0018 REMARK 3 T13: 0.0054 T23: 0.0083 REMARK 3 L TENSOR REMARK 3 L11: 0.4340 L22: 0.5157 REMARK 3 L33: 0.7313 L12: -0.0332 REMARK 3 L13: -0.0800 L23: -0.1497 REMARK 3 S TENSOR REMARK 3 S11: -0.0083 S12: -0.0296 S13: -0.0160 REMARK 3 S21: -0.0082 S22: 0.0162 S23: -0.0023 REMARK 3 S31: 0.0218 S32: 0.0143 S33: -0.0079 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 : B 281 B 378 REMARK 3 ORIGIN FOR THE GROUP (A): 76.9060 76.5060 13.4810 REMARK 3 T TENSOR REMARK 3 T11: 0.0130 T22: -0.0060 REMARK 3 T33: -0.0247 T12: -0.0206 REMARK 3 T13: -0.0252 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 1.2485 L22: 0.4115 REMARK 3 L33: 1.3032 L12: -0.4166 REMARK 3 L13: -0.2367 L23: 0.2330 REMARK 3 S TENSOR REMARK 3 S11: 0.0655 S12: -0.0216 S13: -0.0830 REMARK 3 S21: -0.0072 S22: -0.0108 S23: 0.0129 REMARK 3 S31: 0.0820 S32: 0.0075 S33: -0.0548 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 3M6Z COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB058186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-08; 24-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 78; 78 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 21-ID-G; 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872; 0.97915 REMARK 200 MONOCHROMATOR : SILICON; NULL REMARK 200 OPTICS : BERYLLIUM LENSES; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225; RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 136662 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 28.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 27.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : 0.37900 REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE CITRATE PH 5.5, 0.15M REMARK 280 SODIUM SULFATE, 0.01M MGCL2, 1 M GUANIDIUM HYDROCHLORIDE, 28% PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 31.82000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.61000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.61000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.82000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.05500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 SER A 376 REMARK 465 ILE A 377 REMARK 465 ALA A 378 REMARK 465 GLY A 379 REMARK 465 ILE A 380 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 LEU B 3 REMARK 465 ASP B 121 REMARK 465 GLU B 122 REMARK 465 ARG B 270 REMARK 465 HIS B 271 REMARK 465 PHE B 374 REMARK 465 GLU B 375 REMARK 465 SER B 376 REMARK 465 ILE B 377 REMARK 465 ALA B 378 REMARK 465 GLY B 379 REMARK 465 ILE B 380 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 11.88 -145.65 REMARK 500 VAL A 125 68.92 33.32 REMARK 500 VAL A 133 -71.68 -115.08 REMARK 500 ALA A 167 -119.28 -134.11 REMARK 500 SER A 222 -168.53 -102.34 REMARK 500 ASP B 75 23.56 -155.40 REMARK 500 VAL B 125 71.48 45.48 REMARK 500 VAL B 133 -80.20 -114.08 REMARK 500 ALA B 167 -114.26 -140.49 REMARK 500 ASP B 178 58.89 39.54 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 493 DISTANCE = 5.60 ANGSTROMS REMARK 525 HOH B 520 DISTANCE = 5.61 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 MG A 385 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 266 O REMARK 620 2 LEU A 269 O 94.8 REMARK 620 3 HOH A 494 O 93.9 128.9 REMARK 620 4 HOH A 495 O 148.2 91.0 59.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 382 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 385 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 386 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 387 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 388 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 389 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 382 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 383 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 385 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI B 386 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 REMARK 900 TOPOISOMERASE V WITH GUANIDIUM HYDROCHLORIDE IN A DIFFERENT REMARK 900 CRYSTALLIZATION CONDITION. REMARK 900 RELATED ID: 3M7D RELATED DB: PDB REMARK 900 RELATED ID: 3M7G RELATED DB: PDB DBREF 3M6Z A 1 380 UNP Q977W1 Q977W1_METKA 1 380 DBREF 3M6Z B 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 SEQRES 1 B 380 MET ALA LEU VAL TYR ASP ALA GLU PHE VAL GLY SER GLU SEQRES 2 B 380 ARG GLU PHE GLU GLU GLU ARG GLU THR PHE LEU LYS GLY SEQRES 3 B 380 VAL LYS ALA TYR ASP GLY VAL LEU ALA THR ARG TYR LEU SEQRES 4 B 380 MET GLU ARG SER SER SER ALA LYS ASN ASP GLU GLU LEU SEQRES 5 B 380 LEU GLU LEU HIS GLN ASN PHE ILE LEU LEU THR GLY SER SEQRES 6 B 380 TYR ALA CYS SER ILE ASP PRO THR GLU ASP ARG TYR GLN SEQRES 7 B 380 ASN VAL ILE VAL ARG GLY VAL ASN PHE ASP GLU ARG VAL SEQRES 8 B 380 GLN ARG LEU SER THR GLY GLY SER PRO ALA ARG TYR ALA SEQRES 9 B 380 ILE VAL TYR ARG ARG GLY TRP ARG ALA ILE ALA LYS ALA SEQRES 10 B 380 LEU ASP ILE ASP GLU GLU ASP VAL PRO ALA ILE GLU VAL SEQRES 11 B 380 ARG ALA VAL LYS ARG ASN PRO LEU GLN PRO ALA LEU TYR SEQRES 12 B 380 ARG ILE LEU VAL ARG TYR GLY ARG VAL ASP LEU MET PRO SEQRES 13 B 380 VAL THR VAL ASP GLU VAL PRO PRO GLU MET ALA GLY GLU SEQRES 14 B 380 PHE GLU ARG LEU ILE GLU ARG TYR ASP VAL PRO ILE ASP SEQRES 15 B 380 GLU LYS GLU GLU ARG ILE LEU GLU ILE LEU ARG GLU ASN SEQRES 16 B 380 PRO TRP THR PRO HIS ASP GLU ILE ALA ARG ARG LEU GLY SEQRES 17 B 380 LEU SER VAL SER GLU VAL GLU GLY GLU LYS ASP PRO GLU SEQRES 18 B 380 SER SER GLY ILE TYR SER LEU TRP SER ARG VAL VAL VAL SEQRES 19 B 380 ASN ILE GLU TYR ASP GLU ARG THR ALA LYS ARG HIS VAL SEQRES 20 B 380 LYS ARG ARG ASP ARG LEU LEU GLU GLU LEU TYR GLU HIS SEQRES 21 B 380 LEU GLU GLU LEU SER GLU ARG TYR LEU ARG HIS PRO LEU SEQRES 22 B 380 THR ARG ARG TRP ILE VAL GLU HIS LYS ARG ASP ILE MET SEQRES 23 B 380 ARG ARG TYR LEU GLU GLN ARG ILE VAL GLU CYS ALA LEU SEQRES 24 B 380 LYS LEU GLN ASP ARG TYR GLY ILE ARG GLU ASP VAL ALA SEQRES 25 B 380 LEU CYS LEU ALA ARG ALA PHE ASP GLY SER ILE SER MET SEQRES 26 B 380 ILE ALA THR THR PRO TYR ARG THR LEU LYS ASP VAL CYS SEQRES 27 B 380 PRO ASP LEU THR LEU GLU GLU ALA LYS SER VAL ASN ARG SEQRES 28 B 380 THR LEU ALA THR LEU ILE ASP GLU HIS GLY LEU SER PRO SEQRES 29 B 380 ASP ALA ALA ASP GLU LEU ILE GLU HIS PHE GLU SER ILE SEQRES 30 B 380 ALA GLY ILE HET PO4 A 381 5 HET PO4 A 382 5 HET PO4 A 383 5 HET MG A 384 1 HET MG A 385 1 HET CL A 386 1 HET CL A 387 1 HET GAI A 388 4 HET GAI A 389 4 HET PO4 B 381 10 HET PO4 B 382 5 HET PO4 B 383 5 HET PO4 B 384 5 HET MG B 385 1 HET GAI B 386 4 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM GAI GUANIDINE FORMUL 3 PO4 7(O4 P 3-) FORMUL 6 MG 3(MG 2+) FORMUL 8 CL 2(CL 1-) FORMUL 10 GAI 3(C H5 N3) FORMUL 18 HOH *573(H2 O) HELIX 1 1 SER A 12 SER A 43 1 32 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 ARG A 109 LEU A 118 1 10 HELIX 7 7 GLN A 139 TYR A 149 1 11 HELIX 8 8 THR A 158 VAL A 162 5 5 HELIX 9 9 PRO A 163 ALA A 167 5 5 HELIX 10 10 GLU A 169 TYR A 177 1 9 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 ARG A 267 1 29 HELIX 16 16 THR A 274 HIS A 281 1 8 HELIX 17 17 HIS A 281 TYR A 305 1 25 HELIX 18 18 ARG A 308 PHE A 319 1 12 HELIX 19 19 SER A 322 ALA A 327 1 6 HELIX 20 20 PRO A 330 CYS A 338 1 9 HELIX 21 21 THR A 342 ASN A 350 1 9 HELIX 22 22 ASN A 350 GLU A 359 1 10 HELIX 23 23 SER A 363 GLU A 375 1 13 HELIX 24 24 SER B 12 GLU B 41 1 30 HELIX 25 25 SER B 43 ASN B 48 1 6 HELIX 26 26 ASP B 49 SER B 69 1 21 HELIX 27 27 PHE B 87 ARG B 93 1 7 HELIX 28 28 SER B 99 VAL B 106 1 8 HELIX 29 29 GLY B 110 LEU B 118 1 9 HELIX 30 30 GLN B 139 TYR B 149 1 11 HELIX 31 31 THR B 158 VAL B 162 5 5 HELIX 32 32 PRO B 163 ALA B 167 5 5 HELIX 33 33 GLU B 169 ARG B 176 1 8 HELIX 34 34 ASP B 182 ASN B 195 1 14 HELIX 35 35 PRO B 199 GLY B 208 1 10 HELIX 36 36 SER B 210 GLY B 216 1 7 HELIX 37 37 GLY B 224 VAL B 234 1 11 HELIX 38 38 ASP B 239 GLU B 266 1 28 HELIX 39 39 THR B 274 HIS B 281 1 8 HELIX 40 40 HIS B 281 TYR B 289 1 9 HELIX 41 41 TYR B 289 GLY B 306 1 18 HELIX 42 42 ARG B 308 PHE B 319 1 12 HELIX 43 43 SER B 322 ALA B 327 1 6 HELIX 44 44 PRO B 330 CYS B 338 1 9 HELIX 45 45 THR B 342 ASN B 350 1 9 HELIX 46 46 ASN B 350 GLU B 359 1 10 HELIX 47 47 SER B 363 HIS B 373 1 11 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 SHEET 1 B 3 ASP B 6 PHE B 9 0 SHEET 2 B 3 TYR B 77 VAL B 82 -1 O ILE B 81 N ASP B 6 SHEET 3 B 3 VAL B 85 ASN B 86 -1 O VAL B 85 N VAL B 82 SSBOND 1 CYS A 314 CYS A 338 1555 1555 2.05 SSBOND 2 CYS B 314 CYS B 338 1555 1555 2.05 LINK O GLU A 266 MG MG A 385 1555 1555 2.32 LINK O LEU A 269 MG MG A 385 1555 1555 2.37 LINK O3 APO4 B 381 MG MG B 385 1555 1555 2.76 LINK O VAL A 349 MG MG A 384 1555 1555 2.91 LINK MG MG A 385 O HOH A 494 1555 1555 2.40 LINK MG MG A 385 O HOH A 495 1555 1555 2.68 SITE 1 AC1 10 ARG A 108 ARG A 131 ARG A 144 ARG A 293 SITE 2 AC1 10 SER A 322 HOH A 428 HOH A 463 HOH A 465 SITE 3 AC1 10 HOH A 538 HOH A 630 SITE 1 AC2 5 ARG A 42 LEU A 269 ARG A 270 HIS A 271 SITE 2 AC2 5 HOH A 599 SITE 1 AC3 6 ARG A 14 ARG A 37 LYS A 47 LYS A 134 SITE 2 AC3 6 ARG A 135 GLN A 292 SITE 1 AC4 5 SER A 210 VAL A 211 VAL A 349 ASN A 350 SITE 2 AC4 5 ARG A 351 SITE 1 AC5 5 GLU A 266 LEU A 269 HOH A 494 HOH A 495 SITE 2 AC5 5 GLU B 15 SITE 1 AC6 6 SER A 12 GLU A 13 ARG A 14 GLU A 50 SITE 2 AC6 6 LEU A 53 HOH A 513 SITE 1 AC7 3 VAL A 4 TYR A 5 LYS A 116 SITE 1 AC8 8 VAL A 133 LYS A 134 ARG A 293 HOH A 440 SITE 2 AC8 8 HOH A 463 HOH A 482 HOH A 630 HOH A 646 SITE 1 AC9 4 ASP A 160 VAL A 162 GLU B 51 GLU B 54 SITE 1 BC1 11 ARG B 108 ARG B 131 VAL B 133 ARG B 144 SITE 2 BC1 11 ARG B 293 SER B 322 SER B 324 MG B 385 SITE 3 BC1 11 HOH B 445 HOH B 449 HOH B 471 SITE 1 BC2 8 ARG B 37 VAL B 133 LYS B 134 ARG B 135 SITE 2 BC2 8 ARG B 293 HOH B 438 HOH B 496 HOH B 666 SITE 1 BC3 8 TYR B 30 ARG B 37 ARG B 108 GLU B 129 SITE 2 BC3 8 ARG B 131 ALA B 132 TYR B 289 ARG B 293 SITE 1 BC4 3 ARG B 172 ARG B 176 HOH B 562 SITE 1 BC5 7 ASP B 201 SER B 322 ILE B 323 SER B 324 SITE 2 BC5 7 PO4 B 381 HOH B 449 HOH B 485 SITE 1 BC6 5 VAL A 10 ASP A 75 HOH A 614 GLU B 169 SITE 2 BC6 5 ARG B 172 CRYST1 63.640 80.110 137.220 90.00 90.00 90.00 P 21 21 21 8 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 0.015713 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012483 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007288 0.00000