HEADER TRANSFERASE 21-APR-06 2DMJ TITLE SOLUTION STRUCTURE OF THE FIRST ZF-PARP DOMAIN OF HUMAN POLY(ADP- TITLE 2 RIBOSE)POLYMERASE-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY (ADP-RIBOSE) POLYMERASE FAMILY, MEMBER 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZF-PARP; COMPND 5 SYNONYM: POLY (ADP-RIBOSE) POLYMERASE-1; COMPND 6 EC: 2.4.2.30; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: PARP1, ADPRT, PPOL; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050516-17; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS ZINC FINGER, PARP-1, ADPRT, NAD(+) ADP-RIBOSYLTRANSFERASE 1, KEYWDS 2 POLY(ADP-RIBOSE) SYNTHETASE 1, DNA NICK SENSOR, DNA REPAIR, KEYWDS 3 TRANSCRIPTION, XRCC1, DNA LIGASE III, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 4 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 5 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DMJ 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2DMJ 1 VERSN REVDAT 1 24-APR-07 2DMJ 0 JRNL AUTH T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FIRST ZF-PARP DOMAIN OF HUMAN JRNL TITL 2 POLY(ADP-RIBOSE)POLYMERASE-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DMJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025590. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.02MM UNIFORMLY 13C, 15N REMARK 210 LABELED PROTEIN; 20MM MALONIC REMARK 210 ACID, 100MM NACL, 0.1MM DTT, REMARK 210 0.02% NAN3, 0.05MM ZNCL2, 1MM REMARK 210 NTA; 10% D2O, 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20020425, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9318, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 1 ASP A 13 45.79 -81.89 REMARK 500 1 ALA A 21 143.68 -35.91 REMARK 500 1 LYS A 30 -43.02 -132.20 REMARK 500 1 HIS A 60 157.63 -49.56 REMARK 500 1 PRO A 103 4.29 -69.70 REMARK 500 1 SER A 104 91.33 -43.21 REMARK 500 2 ALA A 21 132.24 -39.68 REMARK 500 2 LYS A 29 30.59 -99.32 REMARK 500 2 LYS A 30 -53.29 -131.61 REMARK 500 2 ASP A 52 39.86 -92.34 REMARK 500 2 PHE A 61 -33.76 -34.02 REMARK 500 2 LEU A 84 153.79 -44.00 REMARK 500 2 PRO A 103 97.01 -69.69 REMARK 500 2 SER A 105 98.54 -56.66 REMARK 500 3 SER A 12 114.61 -161.54 REMARK 500 3 ALA A 21 114.63 -35.12 REMARK 500 3 LYS A 30 -48.75 -133.66 REMARK 500 3 ASP A 52 35.99 33.26 REMARK 500 3 PHE A 61 -37.89 -33.69 REMARK 500 3 PRO A 103 91.16 -69.75 REMARK 500 4 MET A 8 126.28 -38.95 REMARK 500 4 SER A 12 39.25 38.49 REMARK 500 4 ALA A 21 122.67 -33.84 REMARK 500 4 SER A 32 49.30 72.80 REMARK 500 5 SER A 3 114.42 -161.26 REMARK 500 5 SER A 11 44.82 -90.15 REMARK 500 5 ALA A 21 141.63 -33.33 REMARK 500 5 LYS A 30 -54.25 -133.34 REMARK 500 5 SER A 32 54.99 39.98 REMARK 500 5 ASP A 38 48.33 38.97 REMARK 500 5 ASP A 52 38.58 -98.79 REMARK 500 5 PHE A 61 -32.47 -36.22 REMARK 500 5 ARG A 72 -70.20 -62.44 REMARK 500 5 LEU A 84 157.63 -47.08 REMARK 500 5 PRO A 103 -174.46 -69.80 REMARK 500 6 SER A 3 125.29 -174.48 REMARK 500 6 ALA A 9 112.16 -170.40 REMARK 500 6 ASP A 13 47.50 -89.12 REMARK 500 6 LYS A 30 -54.36 -135.00 REMARK 500 6 SER A 32 46.45 72.29 REMARK 500 6 ASP A 52 42.11 -97.11 REMARK 500 6 PHE A 61 -31.87 -39.62 REMARK 500 6 PRO A 103 -173.80 -69.80 REMARK 500 7 ASP A 13 41.85 -97.37 REMARK 500 7 ALA A 26 124.58 -37.27 REMARK 500 7 LYS A 30 -53.41 -130.80 REMARK 500 7 PHE A 61 -30.83 -35.97 REMARK 500 8 SER A 11 -37.47 -134.29 REMARK 500 8 ALA A 21 113.05 -33.50 REMARK 500 8 ALA A 26 157.40 -46.97 REMARK 500 REMARK 500 THIS ENTRY HAS 148 RAMACHANDRAN OUTLIERS. 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 ZN A 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 28 SG REMARK 620 2 CYS A 31 SG 108.2 REMARK 620 3 HIS A 60 ND1 108.1 104.2 REMARK 620 4 CYS A 63 SG 104.9 113.3 117.8 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 ZN A 200 DBREF 2DMJ A 8 100 GB 55663673 CAH70217 1 93 SEQADV 2DMJ GLY A 1 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ SER A 2 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ SER A 3 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ GLY A 4 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ SER A 5 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ SER A 6 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ GLY A 7 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ SER A 101 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ GLY A 102 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ PRO A 103 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ SER A 104 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ SER A 105 GB 55663673 CLONING ARTIFACT SEQADV 2DMJ GLY A 106 GB 55663673 CLONING ARTIFACT SEQRES 1 A 106 GLY SER SER GLY SER SER GLY MET ALA GLU SER SER ASP SEQRES 2 A 106 LYS LEU TYR ARG VAL GLU TYR ALA LYS SER GLY ARG ALA SEQRES 3 A 106 SER CYS LYS LYS CYS SER GLU SER ILE PRO LYS ASP SER SEQRES 4 A 106 LEU ARG MET ALA ILE MET VAL GLN SER PRO MET PHE ASP SEQRES 5 A 106 GLY LYS VAL PRO HIS TRP TYR HIS PHE SER CYS PHE TRP SEQRES 6 A 106 LYS VAL GLY HIS SER ILE ARG HIS PRO ASP VAL GLU VAL SEQRES 7 A 106 ASP GLY PHE SER GLU LEU ARG TRP ASP ASP GLN GLN LYS SEQRES 8 A 106 VAL LYS LYS THR ALA GLU ALA GLY GLY SER GLY PRO SER SEQRES 9 A 106 SER GLY HET ZN A 200 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 SER A 62 VAL A 67 1 6 HELIX 2 2 ARG A 85 GLY A 99 1 15 SHEET 1 A 2 TYR A 16 ARG A 17 0 SHEET 2 A 2 VAL A 78 ASP A 79 1 O ASP A 79 N TYR A 16 SHEET 1 B 3 GLU A 19 TYR A 20 0 SHEET 2 B 3 LEU A 40 SER A 48 -1 O ARG A 41 N GLU A 19 SHEET 3 B 3 GLY A 53 HIS A 60 -1 O HIS A 57 N ILE A 44 LINK SG CYS A 28 ZN ZN A 200 1555 1555 2.35 LINK SG CYS A 31 ZN ZN A 200 1555 1555 2.34 LINK ND1 HIS A 60 ZN ZN A 200 1555 1555 2.08 LINK SG CYS A 63 ZN ZN A 200 1555 1555 2.25 SITE 1 AC1 4 CYS A 28 CYS A 31 HIS A 60 CYS A 63 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20