HEADER ISOMERASE/DNA 20-DEC-09 3L4K TITLE TOPOISOMERASE II-DNA CLEAVAGE COMPLEX, METAL-BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 421-1177; COMPND 5 SYNONYM: DNA TOPOISOMERASE II; COMPND 6 EC: 5.99.1.3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)- COMPND 14 3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*)-3'); COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)- COMPND 23 3'); COMPND 24 CHAIN: E; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: N2244, TOP2, TOR3, YNL088W; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BCY123; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGAL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 MOL_ID: 4; SOURCE 16 SYNTHETIC: YES; SOURCE 17 MOL_ID: 5; SOURCE 18 SYNTHETIC: YES KEYWDS TOPOISOMERASE, PROTEIN-DNA COMPLEX, COVALENTLY LINKED COMPLEX, DNA KEYWDS 2 SUPERCOILING, DNA REPLICATION, ATP-BINDING, DNA-BINDING, ISOMERASE, KEYWDS 3 NUCLEOTIDE-BINDING, NUCLEUS, PHOSPHOPROTEIN, ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.H.SCHMIDT,A.B.BURGIN,J.E.DEWEESE,N.OSHEROFF,J.M.BERGER REVDAT 8 16-OCT-24 3L4K 1 REMARK REVDAT 7 22-NOV-23 3L4K 1 REMARK REVDAT 6 06-SEP-23 3L4K 1 REMARK LINK REVDAT 5 31-JUL-19 3L4K 1 LINK REVDAT 4 13-SEP-17 3L4K 1 REMARK REVDAT 3 16-JUN-10 3L4K 1 JRNL REVDAT 2 09-JUN-10 3L4K 1 JRNL REVDAT 1 26-MAY-10 3L4K 0 JRNL AUTH B.H.SCHMIDT,A.B.BURGIN,J.E.DEWEESE,N.OSHEROFF,J.M.BERGER JRNL TITL A NOVEL AND UNIFIED TWO-METAL MECHANISM FOR DNA CLEAVAGE BY JRNL TITL 2 TYPE II AND IA TOPOISOMERASES. JRNL REF NATURE V. 465 641 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20485342 JRNL DOI 10.1038/NATURE08974 REMARK 2 REMARK 2 RESOLUTION. 2.98 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) : 2.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.900 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 3 NUMBER OF REFLECTIONS : 17619 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1549 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 49.0292 - 6.6297 0.85 2643 148 0.1935 0.2090 REMARK 3 2 6.6297 - 5.2641 0.85 2683 113 0.2130 0.2677 REMARK 3 3 5.2641 - 4.5993 0.85 2659 132 0.1961 0.1875 REMARK 3 4 4.5993 - 4.1790 0.85 2660 139 0.1971 0.2457 REMARK 3 5 4.1790 - 3.8796 0.86 2687 137 0.2291 0.2826 REMARK 3 6 3.8796 - 3.6510 0.87 2716 157 0.2549 0.2904 REMARK 3 7 3.6510 - 3.4682 0.87 2706 143 0.2725 0.3470 REMARK 3 8 3.4682 - 3.3172 0.87 2705 171 0.2990 0.3261 REMARK 3 9 3.3172 - 3.1895 0.88 2710 153 0.3276 0.3980 REMARK 3 10 3.1895 - 3.0795 0.88 2740 129 0.3301 0.3650 REMARK 3 11 3.0795 - 2.9800 0.86 2722 127 0.3373 0.3943 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 : 0.27 REMARK 3 B_SOL : 30.23 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 89.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.86590 REMARK 3 B22 (A**2) : 14.00890 REMARK 3 B33 (A**2) : -5.14300 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 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 : 0.008 7257 REMARK 3 ANGLE : 1.250 10013 REMARK 3 CHIRALITY : 0.103 1079 REMARK 3 PLANARITY : 0.007 1096 REMARK 3 DIHEDRAL : 18.072 2802 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FRIEDEL PAIRS WERE USED FOR PHASING REMARK 4 REMARK 4 3L4K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000056824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 1.2823 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18071 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.53800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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 2RGR REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% 1,4-BUTANEDIOL, 0.1M SODIUM REMARK 280 ACETATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 43.03200 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.96950 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.03200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.96950 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 116 LIES ON A SPECIAL POSITION. 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 PRO A 1071 REMARK 465 ASN A 1072 REMARK 465 ASP A 1073 REMARK 465 GLU A 1074 REMARK 465 ILE A 1075 REMARK 465 ALA A 1076 REMARK 465 GLU A 1077 REMARK 465 GLN A 1078 REMARK 465 ILE A 1079 REMARK 465 ASN A 1080 REMARK 465 ASP A 1081 REMARK 465 VAL A 1082 REMARK 465 LYS A 1083 REMARK 465 GLY A 1084 REMARK 465 ALA A 1085 REMARK 465 THR A 1086 REMARK 465 SER A 1087 REMARK 465 ASP A 1088 REMARK 465 GLU A 1089 REMARK 465 GLU A 1090 REMARK 465 ASP A 1091 REMARK 465 GLU A 1092 REMARK 465 GLU A 1093 REMARK 465 SER A 1094 REMARK 465 SER A 1095 REMARK 465 HIS A 1096 REMARK 465 GLU A 1097 REMARK 465 ASP A 1098 REMARK 465 THR A 1099 REMARK 465 GLU A 1100 REMARK 465 ASN A 1101 REMARK 465 VAL A 1102 REMARK 465 ILE A 1103 REMARK 465 ASN A 1104 REMARK 465 GLY A 1105 REMARK 465 PRO A 1106 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 DC C 1 O5' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 571 CD PRO A 571 N -0.088 REMARK 500 ARG A 781 C PTR A 782 N 0.218 REMARK 500 DC B 2 P DC B 2 OP2 -0.210 REMARK 500 DC C 1 O3' DG C 2 P -0.140 REMARK 500 DA D 6 P DA D 6 OP2 -0.131 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 PRO A 571 N - CA - C ANGL. DEV. = 17.2 DEGREES REMARK 500 THR A 572 N - CA - CB ANGL. DEV. = 13.2 DEGREES REMARK 500 DC B 2 O5' - P - OP2 ANGL. DEV. = -7.4 DEGREES REMARK 500 DT B 6 O5' - P - OP1 ANGL. DEV. = 13.9 DEGREES REMARK 500 DT B 6 O5' - P - OP2 ANGL. DEV. = -18.9 DEGREES REMARK 500 DA B 10 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DA B 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG D 2 O3' - P - OP2 ANGL. DEV. = -19.9 DEGREES REMARK 500 DG D 2 O3' - P - OP1 ANGL. DEV. = 7.8 DEGREES REMARK 500 DA D 6 O3' - P - OP2 ANGL. DEV. = 12.2 DEGREES REMARK 500 DA D 6 O5' - P - OP1 ANGL. DEV. = 14.4 DEGREES REMARK 500 DA D 6 O5' - P - OP2 ANGL. DEV. = -18.5 DEGREES REMARK 500 DA D 6 O5' - C5' - C4' ANGL. DEV. = 25.9 DEGREES REMARK 500 DT D 10 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DT D 10 O4' - C1' - N1 ANGL. DEV. = 3.5 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 VAL A 481 1.30 -69.42 REMARK 500 LYS A 508 -139.93 58.92 REMARK 500 GLN A 527 15.75 86.95 REMARK 500 THR A 572 116.61 -162.30 REMARK 500 GLU A 591 -31.52 -130.88 REMARK 500 LEU A 605 -5.75 85.22 REMARK 500 SER A 608 125.51 -37.78 REMARK 500 LYS A 644 3.52 -61.66 REMARK 500 LYS A 668 8.13 86.86 REMARK 500 GLU A 679 -60.19 -123.91 REMARK 500 SER A 755 -154.10 -110.59 REMARK 500 LYS A 811 141.71 -170.67 REMARK 500 VAL A 813 -152.37 -120.77 REMARK 500 LEU A 882 10.72 80.82 REMARK 500 ASP A 895 109.47 -57.20 REMARK 500 ASP A 938 -89.07 -109.47 REMARK 500 LYS A1036 15.42 86.59 REMARK 500 ASN A1042 -146.03 63.86 REMARK 500 LYS A1043 107.29 59.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 TSP D 11 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 735 NE2 REMARK 620 2 GLU A 808 OE2 99.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 449 OE2 REMARK 620 2 ASP A 526 OD2 60.1 REMARK 620 3 DC B 11 O3' 122.8 138.3 REMARK 620 4 TSP D 11 S3' 127.8 137.3 5.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 4 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 526 OD2 REMARK 620 2 ASP A 528 OD2 97.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 16 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 4 N7 REMARK 620 2 DG E 4 N7 2.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TSP D 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN E 16 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3L4J RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT ZINC IONS SOAKED IN DBREF 3L4K A 421 1177 UNP P06786 TOP2_YEAST 421 1177 DBREF 3L4K B 1 11 PDB 3L4K 3L4K 1 11 DBREF 3L4K C 1 15 PDB 3L4K 3L4K 1 15 DBREF 3L4K D 1 10 PDB 3L4K 3L4K 1 10 DBREF 3L4K E 1 15 PDB 3L4K 3L4K 1 15 SEQADV 3L4K PTR A 782 UNP P06786 TYR 782 MICROHETEROGENEITY SEQRES 1 A 757 SER ARG ILE THR ASN TYR PRO LYS LEU GLU ASP ALA ASN SEQRES 2 A 757 LYS ALA GLY THR LYS GLU GLY TYR LYS CYS THR LEU VAL SEQRES 3 A 757 LEU THR GLU GLY ASP SER ALA LEU SER LEU ALA VAL ALA SEQRES 4 A 757 GLY LEU ALA VAL VAL GLY ARG ASP TYR TYR GLY CYS TYR SEQRES 5 A 757 PRO LEU ARG GLY LYS MET LEU ASN VAL ARG GLU ALA SER SEQRES 6 A 757 ALA ASP GLN ILE LEU LYS ASN ALA GLU ILE GLN ALA ILE SEQRES 7 A 757 LYS LYS ILE MET GLY LEU GLN HIS ARG LYS LYS TYR GLU SEQRES 8 A 757 ASP THR LYS SER LEU ARG TYR GLY HIS LEU MET ILE MET SEQRES 9 A 757 THR ASP GLN ASP HIS ASP GLY SER HIS ILE LYS GLY LEU SEQRES 10 A 757 ILE ILE ASN PHE LEU GLU SER SER PHE PRO GLY LEU LEU SEQRES 11 A 757 ASP ILE GLN GLY PHE LEU LEU GLU PHE ILE THR PRO ILE SEQRES 12 A 757 ILE LYS VAL SER ILE THR LYS PRO THR LYS ASN THR ILE SEQRES 13 A 757 ALA PHE TYR ASN MET PRO ASP TYR GLU LYS TRP ARG GLU SEQRES 14 A 757 GLU GLU SER HIS LYS PHE THR TRP LYS GLN LYS TYR TYR SEQRES 15 A 757 LYS GLY LEU GLY THR SER LEU ALA GLN GLU VAL ARG GLU SEQRES 16 A 757 TYR PHE SER ASN LEU ASP ARG HIS LEU LYS ILE PHE HIS SEQRES 17 A 757 SER LEU GLN GLY ASN ASP LYS ASP TYR ILE ASP LEU ALA SEQRES 18 A 757 PHE SER LYS LYS LYS ALA ASP ASP ARG LYS GLU TRP LEU SEQRES 19 A 757 ARG GLN TYR GLU PRO GLY THR VAL LEU ASP PRO THR LEU SEQRES 20 A 757 LYS GLU ILE PRO ILE SER ASP PHE ILE ASN LYS GLU LEU SEQRES 21 A 757 ILE LEU PHE SER LEU ALA ASP ASN ILE ARG SER ILE PRO SEQRES 22 A 757 ASN VAL LEU ASP GLY PHE LYS PRO GLY GLN ARG LYS VAL SEQRES 23 A 757 LEU TYR GLY CYS PHE LYS LYS ASN LEU LYS SER GLU LEU SEQRES 24 A 757 LYS VAL ALA GLN LEU ALA PRO TYR VAL SER GLU CYS THR SEQRES 25 A 757 ALA TYR HIS HIS GLY GLU GLN SER LEU ALA GLN THR ILE SEQRES 26 A 757 ILE GLY LEU ALA GLN ASN PHE VAL GLY SER ASN ASN ILE SEQRES 27 A 757 TYR LEU LEU LEU PRO ASN GLY ALA PHE GLY THR ARG ALA SEQRES 28 A 757 THR GLY GLY LYS ASP ALA ALA ALA ALA ARG PTR ILE TYR SEQRES 29 A 757 THR GLU LEU ASN LYS LEU THR ARG LYS ILE PHE HIS PRO SEQRES 30 A 757 ALA ASP ASP PRO LEU TYR LYS TYR ILE GLN GLU ASP GLU SEQRES 31 A 757 LYS THR VAL GLU PRO GLU TRP TYR LEU PRO ILE LEU PRO SEQRES 32 A 757 MET ILE LEU VAL ASN GLY ALA GLU GLY ILE GLY THR GLY SEQRES 33 A 757 TRP SER THR TYR ILE PRO PRO PHE ASN PRO LEU GLU ILE SEQRES 34 A 757 ILE LYS ASN ILE ARG HIS LEU MET ASN ASP GLU GLU LEU SEQRES 35 A 757 GLU GLN MET HIS PRO TRP PHE ARG GLY TRP THR GLY THR SEQRES 36 A 757 ILE GLU GLU ILE GLU PRO LEU ARG TYR ARG MET TYR GLY SEQRES 37 A 757 ARG ILE GLU GLN ILE GLY ASP ASN VAL LEU GLU ILE THR SEQRES 38 A 757 GLU LEU PRO ALA ARG THR TRP THR SER THR ILE LYS GLU SEQRES 39 A 757 TYR LEU LEU LEU GLY LEU SER GLY ASN ASP LYS ILE LYS SEQRES 40 A 757 PRO TRP ILE LYS ASP MET GLU GLU GLN HIS ASP ASP ASN SEQRES 41 A 757 ILE LYS PHE ILE ILE THR LEU SER PRO GLU GLU MET ALA SEQRES 42 A 757 LYS THR ARG LYS ILE GLY PHE TYR GLU ARG PHE LYS LEU SEQRES 43 A 757 ILE SER PRO ILE SER LEU MET ASN MET VAL ALA PHE ASP SEQRES 44 A 757 PRO HIS GLY LYS ILE LYS LYS TYR ASN SER VAL ASN GLU SEQRES 45 A 757 ILE LEU SER GLU PHE TYR TYR VAL ARG LEU GLU TYR TYR SEQRES 46 A 757 GLN LYS ARG LYS ASP HIS MET SER GLU ARG LEU GLN TRP SEQRES 47 A 757 GLU VAL GLU LYS TYR SER PHE GLN VAL LYS PHE ILE LYS SEQRES 48 A 757 MET ILE ILE GLU LYS GLU LEU THR VAL THR ASN LYS PRO SEQRES 49 A 757 ARG ASN ALA ILE ILE GLN GLU LEU GLU ASN LEU GLY PHE SEQRES 50 A 757 PRO ARG PHE ASN LYS GLU GLY LYS PRO TYR TYR GLY SER SEQRES 51 A 757 PRO ASN ASP GLU ILE ALA GLU GLN ILE ASN ASP VAL LYS SEQRES 52 A 757 GLY ALA THR SER ASP GLU GLU ASP GLU GLU SER SER HIS SEQRES 53 A 757 GLU ASP THR GLU ASN VAL ILE ASN GLY PRO GLU GLU LEU SEQRES 54 A 757 TYR GLY THR TYR GLU TYR LEU LEU GLY MET ARG ILE TRP SEQRES 55 A 757 SER LEU THR LYS GLU ARG TYR GLN LYS LEU LEU LYS GLN SEQRES 56 A 757 LYS GLN GLU LYS GLU THR GLU LEU GLU ASN LEU LEU LYS SEQRES 57 A 757 LEU SER ALA LYS ASP ILE TRP ASN THR ASP LEU LYS ALA SEQRES 58 A 757 PHE GLU VAL GLY TYR GLN GLU PHE LEU GLN ARG ASP ALA SEQRES 59 A 757 GLU ALA ARG SEQRES 1 B 11 DC DC DT DA DC DT DG DC DT DA DC SEQRES 1 C 15 DC DG DC DG DG DT DA DG DC DA DG DT DA SEQRES 2 C 15 DG DG SEQRES 1 D 10 DG DG DA DT DG DA DC DG DA DT SEQRES 1 E 15 DC DG DC DG DA DA DT DC DG DT DC DA DT SEQRES 2 E 15 DC DC MODRES 3L4K PTR A 782 TYR O-PHOSPHOTYROSINE HET PTR A 782 16 HET ZN A 1 1 HET ZN A 3 1 HET ZN A 4 1 HET ZN A 5 1 HET ZN A 6 1 HET ZN A 7 1 HET ZN A 8 1 HET TSP D 11 20 HET ZN E 16 1 HETNAM PTR O-PHOSPHOTYROSINE HETNAM ZN ZINC ION HETNAM TSP 3'-THIO-THYMIDINE-5'-PHOSPHATE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 PTR C9 H12 N O6 P FORMUL 6 ZN 8(ZN 2+) FORMUL 13 TSP C10 H15 N2 O7 P S FORMUL 15 HOH *20(H2 O) HELIX 1 1 GLY A 450 GLY A 465 1 16 HELIX 2 2 SER A 485 ASN A 492 1 8 HELIX 3 3 ASN A 492 GLY A 503 1 12 HELIX 4 4 ASP A 512 LEU A 516 5 5 HELIX 5 5 ASP A 528 PHE A 546 1 19 HELIX 6 6 ASN A 580 GLU A 591 1 12 HELIX 7 7 SER A 592 PHE A 595 5 4 HELIX 8 8 VAL A 613 ASN A 619 1 7 HELIX 9 9 LEU A 620 ARG A 622 5 3 HELIX 10 10 ASN A 633 SER A 643 1 11 HELIX 11 11 LYS A 646 TYR A 657 1 12 HELIX 12 12 ILE A 672 ASN A 677 1 6 HELIX 13 13 GLU A 679 ILE A 692 1 14 HELIX 14 14 LYS A 700 LYS A 713 1 14 HELIX 15 15 VAL A 721 THR A 732 1 12 HELIX 16 16 GLY A 737 GLN A 750 1 14 HELIX 17 17 LEU A 790 PHE A 795 1 6 HELIX 18 18 HIS A 796 TYR A 803 5 8 HELIX 19 19 PRO A 823 GLY A 829 1 7 HELIX 20 20 ASN A 845 ASN A 858 1 14 HELIX 21 21 TRP A 908 GLY A 922 1 15 HELIX 22 22 SER A 948 GLY A 959 1 12 HELIX 23 23 GLY A 959 PHE A 964 1 6 HELIX 24 24 SER A 989 LYS A 1036 1 48 HELIX 25 25 PRO A 1044 LEU A 1055 1 12 HELIX 26 26 TYR A 1113 GLY A 1118 1 6 HELIX 27 27 ARG A 1120 LEU A 1124 5 5 HELIX 28 28 THR A 1125 LYS A 1148 1 24 HELIX 29 29 SER A 1150 ALA A 1176 1 27 SHEET 1 A 6 TYR A 469 LEU A 474 0 SHEET 2 A 6 THR A 444 GLU A 449 1 N VAL A 446 O GLY A 470 SHEET 3 A 6 HIS A 520 MET A 524 1 O MET A 522 N LEU A 447 SHEET 4 A 6 LEU A 556 PHE A 559 1 O LEU A 557 N LEU A 521 SHEET 5 A 6 LEU A 624 PHE A 627 -1 O LYS A 625 N GLU A 558 SHEET 6 A 6 GLU A 669 ILE A 670 1 O ILE A 670 N ILE A 626 SHEET 1 B 3 THR A 575 PHE A 578 0 SHEET 2 B 3 ILE A 564 ILE A 568 -1 N VAL A 566 O ILE A 576 SHEET 3 B 3 TRP A 597 TYR A 601 -1 O LYS A 598 N SER A 567 SHEET 1 C 2 LEU A 719 LYS A 720 0 SHEET 2 C 2 TYR A 784 THR A 785 -1 O THR A 785 N LEU A 719 SHEET 1 D 2 TYR A 805 GLN A 807 0 SHEET 2 D 2 THR A 812 PRO A 815 -1 O VAL A 813 N ILE A 806 SHEET 1 E 2 ALA A 830 ILE A 833 0 SHEET 2 E 2 SER A 838 ILE A 841 -1 O ILE A 841 N ALA A 830 SHEET 1 F 3 THR A 875 GLU A 878 0 SHEET 2 F 3 ARG A 883 TYR A 887 -1 O TYR A 887 N THR A 875 SHEET 3 F 3 ILE A 967 SER A 971 -1 O SER A 968 N MET A 886 SHEET 1 G 4 ARG A 889 GLY A 894 0 SHEET 2 G 4 VAL A 897 GLU A 902 -1 O GLU A 899 N GLU A 891 SHEET 3 G 4 PHE A 943 THR A 946 -1 O ILE A 945 N LEU A 898 SHEET 4 G 4 ASP A 932 GLU A 935 -1 N ASP A 932 O THR A 946 SHEET 1 H 2 MET A 975 PHE A 978 0 SHEET 2 H 2 ILE A 984 TYR A 987 -1 O TYR A 987 N MET A 975 SHEET 1 I 2 ARG A1059 PHE A1060 0 SHEET 2 I 2 PRO A1066 TYR A1067 -1 O TYR A1067 N ARG A1059 LINK C ARG A 781 N APTR A 782 1555 1555 1.55 LINK C APTR A 782 N ILE A 783 1555 1555 1.41 LINK ZN ZN A 1 NE2 HIS A 735 1555 1555 1.94 LINK ZN ZN A 1 OE2 GLU A 808 1555 1555 2.07 LINK ZN ZN A 3 OE2 GLU A 449 1555 1555 2.69 LINK ZN ZN A 3 OD2 ASP A 526 1555 1555 2.22 LINK ZN ZN A 3 O3'A DC B 11 1555 1555 2.08 LINK ZN ZN A 3 S3'BTSP D 11 1555 1555 2.05 LINK ZN ZN A 4 OD2 ASP A 526 1555 1555 2.30 LINK ZN ZN A 4 OD2 ASP A 528 1555 1555 2.12 LINK ZN ZN A 5 NE2 HIS A 981 1555 1555 2.36 LINK ZN ZN A 6 NE2 HIS A 623 1555 1555 2.46 LINK ZN ZN A 7 NE2 HIS A 628 1555 1555 2.65 LINK ZN ZN A 8 NE2 HIS A 736 1555 1555 2.50 LINK N7 A DG C 4 ZN ZN E 16 1555 1555 1.96 LINK N7 B DG E 4 ZN ZN E 16 1555 1555 1.92 SITE 1 AC1 3 HIS A 735 GLU A 808 ASP A 809 SITE 1 AC2 6 ZN A 4 GLU A 449 ASP A 526 PTR A 782 SITE 2 AC2 6 DC B 11 TSP D 11 SITE 1 AC3 4 ZN A 3 ASP A 526 ASP A 528 LYS A 603 SITE 1 AC4 2 HIS A 981 GLU A1175 SITE 1 AC5 3 GLU A 615 HIS A 623 ASP A 859 SITE 1 AC6 3 GLN A 553 HIS A 628 GLU A 669 SITE 1 AC7 1 HIS A 736 SITE 1 AC8 14 ZN A 3 GLU A 449 LYS A 477 ASP A 530 SITE 2 AC8 14 HIS A 736 GLY A 737 PTR A 782 DC C 1 SITE 3 AC8 14 DG C 5 DT C 6 DT D 10 DC E 1 SITE 4 AC8 14 DA E 5 DA E 6 SITE 1 AC9 2 DG C 4 DG E 4 CRYST1 86.064 91.851 115.939 90.00 90.00 90.00 P 21 2 21 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 0.011619 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008625 0.00000