HEADER TRANSFERASE 10-FEB-00 1EFY TITLE CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF POLY (ADP-RIBOSE) TITLE 2 POLYMERASE COMPLEXED WITH A BENZIMIDAZOLE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY (ADP-RIBOSE) POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC FRAGMENT; COMPND 5 EC: 2.4.2.30; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: BACULOVIRUS KEYWDS BENZIMIDAZOLE, INHIBITOR, CATALYTIC FRAGMENT, POLYMERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.W.WHITE,R.ALMASSY,A.H.CALVERT,N.J.CURTIN,R.J.GRIFFIN,Z.HOSTOMSKY, AUTHOR 2 K.MAEGLEY,D.R.NEWELL,S.SRINIVASAN,B.T.GOLDING REVDAT 5 07-FEB-24 1EFY 1 REMARK REVDAT 4 04-OCT-17 1EFY 1 REMARK REVDAT 3 24-FEB-09 1EFY 1 VERSN REVDAT 2 01-APR-03 1EFY 1 JRNL REVDAT 1 17-JAN-01 1EFY 0 JRNL AUTH A.W.WHITE,R.ALMASSY,A.H.CALVERT,N.J.CURTIN,R.J.GRIFFIN, JRNL AUTH 2 Z.HOSTOMSKY,K.MAEGLEY,D.R.NEWELL,S.SRINIVASAN,B.T.GOLDING JRNL TITL RESISTANCE-MODIFYING AGENTS. 9. SYNTHESIS AND BIOLOGICAL JRNL TITL 2 PROPERTIES OF BENZIMIDAZOLE INHIBITORS OF THE DNA REPAIR JRNL TITL 3 ENZYME POLY(ADP-RIBOSE) POLYMERASE. JRNL REF J.MED.CHEM. V. 43 4084 2000 JRNL REFN ISSN 0022-2623 JRNL PMID 11063605 JRNL DOI 10.1021/JM000950V REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 17889 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1756 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.315 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.59 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.137 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010536. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-97 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18995 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3400, ISOPROPYL ALCOHOL, TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 29.68000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.49000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.49000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.68000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.13000 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 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 MET A 746 35.77 -89.85 REMARK 500 ASN A 782 56.28 -98.63 REMARK 500 GLU A 783 70.15 -119.96 REMARK 500 ASP A 784 -66.46 -132.95 REMARK 500 ASP A 807 46.67 -103.05 REMARK 500 ASN A 827 47.35 -98.22 REMARK 500 MET A 890 -78.62 -37.05 REMARK 500 PHE A 891 39.72 -85.58 REMARK 500 ASP A 914 73.56 -159.28 REMARK 500 SER A 936 116.93 -166.94 REMARK 500 THR A 962 -169.89 -117.16 REMARK 500 ILE A 979 40.05 -84.22 REMARK 500 ASP A 981 33.64 -164.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BZC A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PAW RELATED DB: PDB REMARK 900 RELATED ID: 1PAX RELATED DB: PDB REMARK 900 RELATED ID: 2PAX RELATED DB: PDB REMARK 900 RELATED ID: 3PAX RELATED DB: PDB REMARK 900 RELATED ID: 4PAX RELATED DB: PDB DBREF 1EFY A 662 1011 UNP P26446 PARP1_CHICK 659 1008 SEQRES 1 A 350 LYS SER LYS LEU ALA LYS PRO ILE GLN ASP LEU ILE LYS SEQRES 2 A 350 MET ILE PHE ASP VAL GLU SER MET LYS LYS ALA MET VAL SEQRES 3 A 350 GLU PHE GLU ILE ASP LEU GLN LYS MET PRO LEU GLY LYS SEQRES 4 A 350 LEU SER LYS ARG GLN ILE GLN SER ALA TYR SER ILE LEU SEQRES 5 A 350 ASN GLU VAL GLN GLN ALA VAL SER ASP GLY GLY SER GLU SEQRES 6 A 350 SER GLN ILE LEU ASP LEU SER ASN ARG PHE TYR THR LEU SEQRES 7 A 350 ILE PRO HIS ASP PHE GLY MET LYS LYS PRO PRO LEU LEU SEQRES 8 A 350 SER ASN LEU GLU TYR ILE GLN ALA LYS VAL GLN MET LEU SEQRES 9 A 350 ASP ASN LEU LEU ASP ILE GLU VAL ALA TYR SER LEU LEU SEQRES 10 A 350 ARG GLY GLY ASN GLU ASP GLY ASP LYS ASP PRO ILE ASP SEQRES 11 A 350 ILE ASN TYR GLU LYS LEU ARG THR ASP ILE LYS VAL VAL SEQRES 12 A 350 ASP LYS ASP SER GLU GLU ALA LYS ILE ILE LYS GLN TYR SEQRES 13 A 350 VAL LYS ASN THR HIS ALA ALA THR HIS ASN ALA TYR ASP SEQRES 14 A 350 LEU LYS VAL VAL GLU ILE PHE ARG ILE GLU ARG GLU GLY SEQRES 15 A 350 GLU SER GLN ARG TYR LYS PRO PHE LYS GLN LEU HIS ASN SEQRES 16 A 350 ARG GLN LEU LEU TRP HIS GLY SER ARG THR THR ASN PHE SEQRES 17 A 350 ALA GLY ILE LEU SER GLN GLY LEU ARG ILE ALA PRO PRO SEQRES 18 A 350 GLU ALA PRO VAL THR GLY TYR MET PHE GLY LYS GLY ILE SEQRES 19 A 350 TYR PHE ALA ASP MET VAL SER LYS SER ALA ASN TYR CYS SEQRES 20 A 350 HIS THR SER GLN ALA ASP PRO ILE GLY LEU ILE LEU LEU SEQRES 21 A 350 GLY GLU VAL ALA LEU GLY ASN MET TYR GLU LEU LYS ASN SEQRES 22 A 350 ALA SER HIS ILE THR LYS LEU PRO LYS GLY LYS HIS SER SEQRES 23 A 350 VAL LYS GLY LEU GLY LYS THR ALA PRO ASP PRO THR ALA SEQRES 24 A 350 THR THR THR LEU ASP GLY VAL GLU VAL PRO LEU GLY ASN SEQRES 25 A 350 GLY ILE SER THR GLY ILE ASN ASP THR CYS LEU LEU TYR SEQRES 26 A 350 ASN GLU TYR ILE VAL TYR ASP VAL ALA GLN VAL ASN LEU SEQRES 27 A 350 LYS TYR LEU LEU LYS LEU LYS PHE ASN TYR LYS THR HET BZC A 201 20 HETNAM BZC 2-(3'-METHOXYPHENYL) BENZIMIDAZOLE-4-CARBOXAMIDE FORMUL 2 BZC C15 H13 N3 O2 FORMUL 3 HOH *91(H2 O) HELIX 1 1 ALA A 666 PHE A 677 1 12 HELIX 2 2 ASP A 678 PHE A 689 1 12 HELIX 3 3 PRO A 697 LEU A 701 5 5 HELIX 4 4 SER A 702 ASP A 722 1 21 HELIX 5 5 SER A 725 ILE A 740 1 16 HELIX 6 6 ASN A 754 GLY A 780 1 27 HELIX 7 7 ASP A 788 LEU A 797 1 10 HELIX 8 8 SER A 808 THR A 821 1 14 HELIX 9 9 ALA A 823 ASN A 827 5 5 HELIX 10 10 GLY A 843 LYS A 849 1 7 HELIX 11 11 PRO A 850 LEU A 854 5 5 HELIX 12 12 ARG A 865 THR A 867 5 3 HELIX 13 13 ASN A 868 GLY A 876 1 9 HELIX 14 14 PRO A 885 TYR A 889 5 5 HELIX 15 15 MET A 900 ASN A 906 1 7 HELIX 16 16 TYR A 907 HIS A 909 5 3 HELIX 17 17 PRO A 958 THR A 961 5 4 HELIX 18 18 ASP A 993 ALA A 995 5 3 SHEET 1 A 5 THR A 799 VAL A 803 0 SHEET 2 A 5 TYR A 829 ARG A 841 -1 N ARG A 838 O LYS A 802 SHEET 3 A 5 VAL A 997 TYR A1009 -1 O LYS A1000 N ILE A 839 SHEET 4 A 5 ILE A 916 ALA A 925 -1 O GLY A 917 N LEU A1005 SHEET 5 A 5 ARG A 857 SER A 864 -1 O GLN A 858 N VAL A 924 SHEET 1 B 4 ILE A 895 PHE A 897 0 SHEET 2 B 4 GLU A 988 VAL A 991 -1 N TYR A 989 O PHE A 897 SHEET 3 B 4 SER A 947 GLY A 950 -1 N VAL A 948 O ILE A 990 SHEET 4 B 4 MET A 929 LEU A 932 1 N TYR A 930 O SER A 947 SHEET 1 C 2 THR A 954 PRO A 956 0 SHEET 2 C 2 GLY A 974 SER A 976 -1 O ILE A 975 N ALA A 955 SHEET 1 D 2 THR A 962 LEU A 964 0 SHEET 2 D 2 VAL A 967 VAL A 969 -1 O VAL A 967 N LEU A 964 SITE 1 AC1 9 HOH A 52 GLN A 763 HIS A 862 GLY A 863 SITE 2 AC1 9 TYR A 896 PHE A 897 SER A 904 TYR A 907 SITE 3 AC1 9 GLU A 988 CRYST1 59.360 64.260 96.980 90.00 90.00 90.00 P 21 21 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 0.016846 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010311 0.00000