HEADER ISOMERASE 04-JUL-06 2HKJ TITLE TOPOISOMERASE VI-B BOUND TO RADICICOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE II DNA TOPOISOMERASE VI SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-470; COMPND 5 SYNONYM: TOPOVI-B; COMPND 6 EC: 5.99.1.3; COMPND 7 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, GHKL, DRUG COMPLEX, RADICICOL, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.D.CORBETT,J.M.BERGER REVDAT 5 30-AUG-23 2HKJ 1 REMARK LINK REVDAT 4 13-JUL-11 2HKJ 1 VERSN REVDAT 3 24-FEB-09 2HKJ 1 VERSN REVDAT 2 03-OCT-06 2HKJ 1 JRNL REVDAT 1 29-AUG-06 2HKJ 0 JRNL AUTH K.D.CORBETT,J.M.BERGER JRNL TITL STRUCTURAL BASIS FOR TOPOISOMERASE VI INHIBITION BY THE JRNL TITL 2 ANTI-HSP90 DRUG RADICICOL JRNL REF NUCLEIC ACIDS RES. V. 34 4269 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16920739 JRNL DOI 10.1093/NAR/GKL567 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 35959 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT : 3236 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2452 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 227 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3704 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 355 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 22.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.89000 REMARK 3 B22 (A**2) : -0.60000 REMARK 3 B33 (A**2) : 1.49000 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): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.404 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3814 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5163 ; 1.410 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 460 ; 6.542 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;35.294 ;24.588 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 700 ;14.177 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.960 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 572 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2859 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1830 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2638 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 320 ; 0.147 ; 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): 58 ; 0.292 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.451 ; 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): 2401 ; 1.172 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3772 ; 1.585 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1644 ; 3.062 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1388 ; 4.715 ; 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 10 A 229 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6050 -0.1010 -17.4670 REMARK 3 T TENSOR REMARK 3 T11: -0.0333 T22: -0.0180 REMARK 3 T33: -0.0300 T12: 0.0035 REMARK 3 T13: 0.0130 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.5926 L22: 0.7536 REMARK 3 L33: 0.3298 L12: 0.0306 REMARK 3 L13: 0.0862 L23: 0.0198 REMARK 3 S TENSOR REMARK 3 S11: 0.0236 S12: -0.0101 S13: 0.0233 REMARK 3 S21: 0.0151 S22: -0.0087 S23: -0.0391 REMARK 3 S31: -0.0400 S32: 0.0171 S33: -0.0150 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): 36.4850 -21.2740 6.5450 REMARK 3 T TENSOR REMARK 3 T11: -0.0565 T22: -0.0578 REMARK 3 T33: -0.0937 T12: -0.0198 REMARK 3 T13: -0.0953 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 4.3281 L22: 3.0462 REMARK 3 L33: 4.8944 L12: 0.2829 REMARK 3 L13: 2.3052 L23: 0.7218 REMARK 3 S TENSOR REMARK 3 S11: -0.2012 S12: -0.0603 S13: 0.2196 REMARK 3 S21: 0.1575 S22: 0.0303 S23: -0.2818 REMARK 3 S31: -0.1838 S32: 0.3023 S33: 0.1709 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): 12.9000 -28.1410 -24.7380 REMARK 3 T TENSOR REMARK 3 T11: -0.0368 T22: -0.0081 REMARK 3 T33: -0.0113 T12: 0.0187 REMARK 3 T13: 0.0055 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.7472 L22: 0.9499 REMARK 3 L33: 0.2034 L12: 0.6640 REMARK 3 L13: 0.2502 L23: 0.3645 REMARK 3 S TENSOR REMARK 3 S11: -0.0157 S12: 0.0364 S13: -0.0675 REMARK 3 S21: -0.0098 S22: 0.0238 S23: -0.0471 REMARK 3 S31: 0.0136 S32: -0.0325 S33: -0.0081 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE R-FREE SET IS THE SAME AS IN PDB REMARK 3 ENTRY 1MU5, THE MOLECULAR REPLACEMENT SEARCH MODEL REMARK 4 REMARK 4 2HKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038451. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 80 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) : 1.1157 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39306 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 1MU5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, MG(HCO2)2, PEG 3350, NACL, REMARK 280 MGCL2, 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 46.93950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.69900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.93950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.69900 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 PROTEIN MONOMER IS THE RELEVANT BIOLOGICAL 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 465 SER A 9 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 249 CG CD CE NZ 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 O HOH A 725 O HOH A 856 1.58 REMARK 500 NH1 ARG A 459 O HOH A 771 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 399 O HOH A 756 3544 1.90 REMARK 500 OG SER A 97 O HOH A 811 4544 1.92 REMARK 500 NH2 ARG A 67 OD1 ASN A 442 3554 2.19 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 MET A 412 CG - SD - CE ANGL. DEV. = -16.0 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 -73.31 -112.22 REMARK 500 ASN A 331 59.23 39.84 REMARK 500 LYS A 343 -166.61 -124.15 REMARK 500 GLU A 428 43.78 -102.81 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 A 471 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 105 O REMARK 620 2 HOH A 502 O 88.9 REMARK 620 3 HOH A 553 O 94.6 169.7 REMARK 620 4 HOH A 582 O 78.4 93.0 97.2 REMARK 620 5 HOH A 658 O 96.2 90.8 79.2 173.3 REMARK 620 6 HOH A 688 O 168.6 93.5 85.0 90.3 94.9 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 471 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 472 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RDC A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MU5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE APO STATE REMARK 900 RELATED ID: 1MX0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN A DIMER FORM COMPLEXED WITH AMP-PNP REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS STATE THE RESIDUES Y303D AND D435N ARE REMARK 999 APPARENTLY CAUSED BY STRAIN-SPECIFIC DIFFERENCES BETWEEN REMARK 999 THE STRAIN OF S. SHIBATAE AND THAT USED FOR GENOMIC REMARK 999 SEQUENCING. THE AUTHORS STATE THEY HAVE CLONED THE GENE REMARK 999 SEVERAL TIMES INDEPENDENTLY, AND THE RESIDUES ARE REMARK 999 CONSISTENTLY DIFFERENT FROM THE DATABASE ENTRY. DBREF 2HKJ A 2 470 UNP O05207 TOP6B_SULSH 2 470 SEQADV 2HKJ TYR A 303 UNP O05207 ASP 303 SEE REMARK 999 SEQADV 2HKJ ASP A 435 UNP O05207 ASN 435 SEE REMARK 999 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 MET TYR GLY LEU GLY VAL LYS ALA ALA VAL LEU TYR SEQRES 10 A 469 SER GLN MET 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 MET VAL VAL MET 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 MET 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 HET MG A 471 1 HET DMS A 472 4 HET RDC A 501 25 HETNAM MG MAGNESIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM RDC RADICICOL HETSYN RDC MONORDEN FORMUL 2 MG MG 2+ FORMUL 3 DMS C2 H6 O S FORMUL 4 RDC C18 H17 CL O6 FORMUL 5 HOH *355(H2 O) HELIX 1 1 SER A 11 ASN A 19 1 9 HELIX 2 2 PRO A 20 GLY A 24 5 5 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 ASN A 247 1 11 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 GLU A 152 GLU A 162 0 SHEET 2 A 8 ARG A 138 ASP A 147 -1 N ASP A 147 O GLU A 152 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 ASP A 76 -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 MET 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 O ARG A 105 MG MG A 471 1555 1555 2.21 LINK MG MG A 471 O HOH A 502 1555 1555 2.24 LINK MG MG A 471 O HOH A 553 1555 1555 2.35 LINK MG MG A 471 O HOH A 582 1555 1555 2.25 LINK MG MG A 471 O HOH A 658 1555 1555 2.56 LINK MG MG A 471 O HOH A 688 1555 1555 2.17 SITE 1 AC1 7 ARG A 105 GLY A 106 HOH A 502 HOH A 553 SITE 2 AC1 7 HOH A 582 HOH A 658 HOH A 688 SITE 1 AC2 6 PRO A 309 ALA A 344 TYR A 345 GLN A 346 SITE 2 AC2 6 GLY A 347 HIS A 348 SITE 1 AC3 16 LEU A 39 ASN A 42 ASP A 45 ALA A 46 SITE 2 AC3 16 ASP A 76 GLY A 80 ILE A 81 ALA A 89 SITE 3 AC3 16 PHE A 90 VAL A 112 THR A 170 VAL A 172 SITE 4 AC3 16 HOH A 506 HOH A 508 HOH A 560 HOH A 578 CRYST1 93.879 111.398 54.888 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 0.010652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018219 0.00000