HEADER ISOMERASE 23-SEP-02 1MU5 TITLE STRUCTURE OF TOPOISOMERASE SUBUNIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE II DNA TOPOISOMERASE VI SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 EC: 5.99.1.3; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GHKL ATPASE, HELIX TWO-TURNS HELIX, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.D.CORBETT,J.M.BERGER REVDAT 3 13-JUL-11 1MU5 1 VERSN REVDAT 2 24-FEB-09 1MU5 1 VERSN REVDAT 1 07-JAN-03 1MU5 0 JRNL AUTH K.D.CORBETT,J.M.BERGER JRNL TITL STRUCTURE OF THE TOPOISOMERASE VI-B SUBUNIT: IMPLICATIONS JRNL TITL 2 FOR TYPE II TOPOISOMERASE MECHANISM AND EVOLUTION JRNL REF EMBO J. V. 22 151 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12505993 JRNL DOI 10.1093/EMBOJ/CDG008 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 34608 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT : 3130 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) : 2342 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 224 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3684 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 237 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) : 19.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.01000 REMARK 3 B22 (A**2) : -1.62000 REMARK 3 B33 (A**2) : 2.63000 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): 0.203 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.541 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 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): 3762 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5091 ; 1.311 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 458 ; 4.280 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 737 ;17.841 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 567 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2811 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1839 ; 0.260 ; 0.300 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): 370 ; 0.167 ; 0.500 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 ; 0.338 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.247 ; 0.500 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): 2303 ; 0.734 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3756 ; 1.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1459 ; 2.558 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1335 ; 4.475 ; 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 : 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): 17.4735 55.5798 17.3587 REMARK 3 T TENSOR REMARK 3 T11: 0.1551 T22: 0.1570 REMARK 3 T33: 0.1346 T12: 0.0021 REMARK 3 T13: -0.0037 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.4568 L22: 0.7145 REMARK 3 L33: 0.2223 L12: -0.0405 REMARK 3 L13: 0.0073 L23: 0.0475 REMARK 3 S TENSOR REMARK 3 S11: 0.0263 S12: 0.0154 S13: 0.0041 REMARK 3 S21: -0.0313 S22: -0.0178 S23: -0.0309 REMARK 3 S31: 0.0222 S32: 0.0286 S33: -0.0085 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): 36.6994 76.7733 -6.4591 REMARK 3 T TENSOR REMARK 3 T11: 0.1689 T22: 0.0797 REMARK 3 T33: 0.1022 T12: -0.0338 REMARK 3 T13: 0.1145 T23: 0.0195 REMARK 3 L TENSOR REMARK 3 L11: 5.2598 L22: 2.5606 REMARK 3 L33: 5.1089 L12: -0.7335 REMARK 3 L13: -3.0771 L23: 1.2618 REMARK 3 S TENSOR REMARK 3 S11: -0.3496 S12: 0.1221 S13: -0.3608 REMARK 3 S21: -0.1343 S22: 0.1186 S23: -0.2013 REMARK 3 S31: 0.1039 S32: 0.1137 S33: 0.2309 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): 12.9290 83.5247 24.5945 REMARK 3 T TENSOR REMARK 3 T11: 0.1509 T22: 0.1554 REMARK 3 T33: 0.1558 T12: -0.0140 REMARK 3 T13: -0.0047 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.7291 L22: 0.7139 REMARK 3 L33: 0.2624 L12: -0.5749 REMARK 3 L13: -0.2822 L23: 0.3177 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: -0.0523 S13: 0.0838 REMARK 3 S21: -0.0238 S22: 0.0170 S23: -0.0441 REMARK 3 S31: -0.0023 S32: -0.0079 S33: -0.0112 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 1MU5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-02. REMARK 100 THE RCSB ID CODE IS RCSB017183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.127 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37738 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 16.7000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40500 REMARK 200 FOR SHELL : 2.650 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 53.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3000, TRIS, CALCIUM ACETATE, PH REMARK 280 7.0, MICROBATCH, TEMPERATURE 293K 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 47.04550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.48400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.04550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.48400 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 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 GLY A -1 REMARK 465 ALA A 0 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 465 SER A 97 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 TYR A 95 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 96 OG 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 OD1 ASP A 61 O HOH A 567 2.12 REMARK 500 O HOH A 528 O HOH A 701 2.16 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 45 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 382 CB - CG - OD2 ANGL. DEV. = 5.9 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 -72.36 -115.33 REMARK 500 LYS A 242 22.63 -72.86 REMARK 500 ASP A 251 66.77 -105.10 REMARK 500 GLU A 290 10.57 -64.76 REMARK 500 ASN A 331 61.14 39.18 REMARK 500 GLU A 428 43.46 -96.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG A 37 24.9 L L OUTSIDE RANGE 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 CA A 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 105 O REMARK 620 2 HOH A 635 O 86.5 REMARK 620 3 HOH A 676 O 157.1 115.2 REMARK 620 4 HOH A 686 O 135.5 53.9 67.3 REMARK 620 5 HOH A 479 O 80.7 152.7 82.2 124.3 REMARK 620 6 HOH A 501 O 99.9 93.3 86.7 67.2 65.5 REMARK 620 7 HOH A 614 O 71.4 97.2 97.4 127.0 101.4 165.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 471 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 393 O REMARK 620 2 LEU A 395 O 94.9 REMARK 620 3 HOH A 530 O 80.1 78.2 REMARK 620 4 HOH A 625 O 170.8 86.5 91.3 REMARK 620 5 HOH A 588 O 90.3 81.2 156.3 98.9 REMARK 620 6 HOH A 628 O 83.7 143.5 136.6 100.6 62.4 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 CA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 471 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MX0 RELATED DB: PDB REMARK 900 STRUCTURE OF TOPOISOMERASE SUBUNIT REMARK 999 REMARK 999 SEQUENCE THE AUTHORS STATE THE RESIDUES Y303D AND D435N ARE REMARK 999 APPARENTLY CAUSED BY STRAIN-SPECIFIC DIFFERENCES BETWEEN THE STRAIN REMARK 999 OF S. SHIBATAE AND THAT USED FOR GENOMIC SEQUENCING. THE AUTHORS REMARK 999 STATE THEY HAVE CLONED THE GENE SEVERAL TIMES INDEPENDENTLY, AND REMARK 999 THE RESIDUES ARE CONSISTENTLY DIFFERENT FROM THE DATABASE ENTRY. DBREF 1MU5 A 2 470 UNP O05207 TOP6B_SULSH 2 470 SEQADV 1MU5 GLY A -1 UNP O05207 EXPRESSION TAG SEQADV 1MU5 ALA A 0 UNP O05207 EXPRESSION TAG SEQADV 1MU5 A UNP O05207 MET 1 DELETION SEQADV 1MU5 TYR A 303 UNP O05207 ASP 303 SEE REMARK 999 SEQADV 1MU5 ASP A 435 UNP O05207 ASN 435 SEE REMARK 999 SEQRES 1 A 471 GLY ALA SER ALA LYS GLU LYS PHE THR SER LEU SER PRO SEQRES 2 A 471 ALA GLU PHE PHE LYS ARG ASN PRO GLU LEU ALA GLY PHE SEQRES 3 A 471 PRO ASN PRO ALA ARG ALA LEU TYR GLN THR VAL ARG GLU SEQRES 4 A 471 LEU ILE GLU ASN SER LEU ASP ALA THR ASP VAL HIS GLY SEQRES 5 A 471 ILE LEU PRO ASN ILE LYS ILE THR ILE ASP LEU ILE ASP SEQRES 6 A 471 ASP ALA ARG GLN ILE TYR LYS VAL ASN VAL VAL ASP ASN SEQRES 7 A 471 GLY ILE GLY ILE PRO PRO GLN GLU VAL PRO ASN ALA PHE SEQRES 8 A 471 GLY ARG VAL LEU TYR SER SER LYS TYR VAL ASN ARG GLN SEQRES 9 A 471 THR ARG GLY MET TYR GLY LEU GLY VAL LYS ALA ALA VAL SEQRES 10 A 471 LEU TYR SER GLN MET HIS GLN ASP LYS PRO ILE GLU ILE SEQRES 11 A 471 GLU THR SER PRO VAL ASN SER LYS ARG ILE TYR THR PHE SEQRES 12 A 471 LYS LEU LYS ILE ASP ILE ASN LYS ASN GLU PRO ILE ILE SEQRES 13 A 471 VAL GLU ARG GLY SER VAL GLU ASN THR ARG GLY PHE HIS SEQRES 14 A 471 GLY THR SER VAL ALA ILE SER ILE PRO GLY ASP TRP PRO SEQRES 15 A 471 LYS ALA LYS SER ARG ILE TYR GLU TYR ILE LYS ARG THR SEQRES 16 A 471 TYR ILE ILE THR PRO TYR ALA GLU PHE ILE PHE LYS ASP SEQRES 17 A 471 PRO GLU GLY ASN VAL THR TYR TYR PRO ARG LEU THR ASN SEQRES 18 A 471 LYS ILE PRO LYS PRO PRO GLN GLU VAL LYS PRO HIS PRO SEQRES 19 A 471 TYR GLY VAL ASP ARG GLU GLU ILE LYS ILE LEU ILE ASN SEQRES 20 A 471 ASN LEU LYS ARG ASP TYR THR ILE LYS GLU PHE LEU VAL SEQRES 21 A 471 ASN GLU PHE GLN SER ILE GLY ASP THR THR ALA ASP LYS SEQRES 22 A 471 ILE LEU GLU LEU ALA GLY LEU LYS PRO ASN LYS LYS VAL SEQRES 23 A 471 LYS ASN LEU THR GLU GLU GLU ILE THR ARG LEU VAL GLU SEQRES 24 A 471 THR PHE LYS LYS TYR GLU ASP PHE ARG SER PRO SER ALA SEQRES 25 A 471 ASP SER LEU SER VAL ILE GLY GLU ASP LEU ILE GLU LEU SEQRES 26 A 471 GLY LEU LYS LYS ILE PHE ASN PRO ASP PHE ALA ALA SER SEQRES 27 A 471 ILE THR ARG LYS PRO LYS ALA TYR GLN GLY HIS PRO PHE SEQRES 28 A 471 ILE VAL GLU ALA GLY VAL ALA PHE GLY GLY SER ILE PRO SEQRES 29 A 471 VAL GLY GLU GLU PRO ILE VAL LEU ARG TYR ALA ASN LYS SEQRES 30 A 471 ILE PRO LEU ILE TYR ASP GLU LYS SER ASP VAL ILE TRP SEQRES 31 A 471 LYS VAL VAL GLU GLU LEU ASP TRP LYS ARG TYR GLY ILE SEQRES 32 A 471 GLU SER ASP GLN TYR GLN MET VAL VAL MET VAL HIS LEU SEQRES 33 A 471 CYS SER THR LYS ILE PRO TYR LYS SER ALA GLY LYS GLU SEQRES 34 A 471 SER ILE ALA GLU VAL GLU ASP ILE GLU LYS GLU ILE LYS SEQRES 35 A 471 ASN ALA LEU MET GLU VAL ALA ARG LYS LEU LYS GLN TYR SEQRES 36 A 471 LEU SER GLU LYS ARG LYS GLU GLN GLU ALA LYS LYS LYS SEQRES 37 A 471 LEU LEU ALA HET CA A 1 1 HET CA A 471 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *237(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 ILE A 245 1 9 HELIX 11 11 THR A 253 VAL A 259 1 7 HELIX 12 12 GLY A 266 ALA A 277 1 12 HELIX 13 13 LYS A 284 LEU A 288 5 5 HELIX 14 14 GLU A 291 TYR A 303 1 13 HELIX 15 15 GLY A 318 ASN A 331 1 14 HELIX 16 16 ASP A 382 SER A 385 5 4 HELIX 17 17 ASP A 386 LEU A 395 1 10 HELIX 18 18 ASP A 396 GLY A 401 5 6 HELIX 19 19 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 VAL A 72 O ILE A 174 SHEET 6 A 8 ASN A 55 ASP A 64 -1 N ASP A 61 O LYS A 71 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 5 ILE A 377 LEU A 379 0 SHEET 2 B 5 ILE A 369 ALA A 374 -1 N ALA A 374 O ILE A 377 SHEET 3 B 5 MET A 409 SER A 417 1 O VAL A 411 N ILE A 369 SHEET 4 B 5 HIS A 348 PHE A 358 -1 N GLY A 355 O MET A 412 SHEET 5 B 5 PHE A 334 THR A 339 -1 N PHE A 334 O PHE A 358 SHEET 1 C 5 ILE A 377 LEU A 379 0 SHEET 2 C 5 ILE A 369 ALA A 374 -1 N ALA A 374 O ILE A 377 SHEET 3 C 5 MET A 409 SER A 417 1 O VAL A 411 N ILE A 369 SHEET 4 C 5 HIS A 348 PHE A 358 -1 N GLY A 355 O MET A 412 SHEET 5 C 5 LYS A 343 TYR A 345 -1 N LYS A 343 O PHE A 350 LINK O ARG A 105 CA CA A 1 1555 1555 2.35 LINK O GLU A 393 CA CA A 471 1555 1555 2.34 LINK O LEU A 395 CA CA A 471 1555 1555 2.54 LINK CA CA A 1 O HOH A 635 1555 1555 2.07 LINK CA CA A 1 O HOH A 676 1555 1555 2.01 LINK CA CA A 1 O HOH A 686 1555 1555 2.67 LINK CA CA A 1 O HOH A 479 1555 1555 2.18 LINK CA CA A 471 O HOH A 530 1555 1555 2.45 LINK CA CA A 471 O HOH A 625 1555 1555 2.64 LINK CA CA A 471 O HOH A 588 1555 1555 2.65 LINK CA CA A 471 O HOH A 628 1555 1555 2.79 LINK CA CA A 1 O HOH A 501 1555 1555 3.00 LINK CA CA A 1 O HOH A 614 1555 1555 1.99 SITE 1 AC1 7 ARG A 105 HOH A 479 HOH A 501 HOH A 614 SITE 2 AC1 7 HOH A 635 HOH A 676 HOH A 686 SITE 1 AC2 6 GLU A 393 LEU A 395 HOH A 530 HOH A 588 SITE 2 AC2 6 HOH A 625 HOH A 628 CRYST1 94.091 110.968 54.544 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 0.010628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009012 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018334 0.00000 MASTER 429 0 2 19 18 0 4 6 0 0 0 37 END