10 20 30 40 50 60 70 80 2DMJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 21-APR-06 2DMJ
TITLE SOLUTION STRUCTURE OF THE FIRST ZF-PARP DOMAIN OF HUMAN TITLE 2 POLY(ADP-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, KEYWDS 4 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 5 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 6 INITIATIVE, RSGI
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI)
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 JRNL TITL 2 HUMAN POLY(ADP-RIBOSE)POLYMERASE-1 JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0.17 REMARK 3 AUTHORS : GUNTERT, P. 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 RCSB ID CODE IS RCSB025590.
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_ REMARK 210 13C-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 : VNMR 6.1C, NMRPIPE 20020425, REMARK 210 NMRVIEW 5.0.4, KUJIRA 0.9318, REMARK 210 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 REMARK 210 WITH 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 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 8 LYS A 30 -53.41 -131.90 REMARK 500 8 ASP A 52 46.16 -78.25 REMARK 500 8 LEU A 84 169.92 -46.68 REMARK 500 9 SER A 6 42.17 -87.60 REMARK 500 9 GLU A 10 106.98 -36.61 REMARK 500 9 ALA A 21 111.80 -33.44 REMARK 500 9 LYS A 29 32.04 -98.72 REMARK 500 9 LYS A 30 -50.54 -131.60 REMARK 500 9 ASP A 52 45.11 -78.65 REMARK 500 9 PRO A 103 5.49 -69.80 REMARK 500 10 LYS A 14 177.40 -53.55 REMARK 500 10 ALA A 21 127.96 -33.86 REMARK 500 10 LYS A 29 33.27 -98.07 REMARK 500 10 LYS A 30 -51.13 -132.58 REMARK 500 10 PRO A 49 3.13 -69.79 REMARK 500 10 ASP A 52 44.77 -83.61 REMARK 500 10 PHE A 61 -35.80 -35.56 REMARK 500 10 PHE A 64 -37.67 -38.46 REMARK 500 10 PRO A 103 11.40 -69.81 REMARK 500 10 SER A 104 167.01 -43.18 REMARK 500 11 SER A 12 107.74 -165.55 REMARK 500 11 ASP A 13 42.52 -85.10 REMARK 500 11 ALA A 21 141.12 -33.53 REMARK 500 11 ALA A 26 147.92 -33.62 REMARK 500 11 LYS A 29 31.92 -99.34 REMARK 500 11 LYS A 30 -54.72 -132.71 REMARK 500 11 PRO A 49 3.79 -69.79 REMARK 500 11 ASP A 52 44.14 -90.60 REMARK 500 11 PHE A 61 -35.04 -35.76 REMARK 500 11 HIS A 69 104.16 -33.37 REMARK 500 11 SER A 101 123.75 -38.68 REMARK 500 12 ASP A 13 46.85 -84.42 REMARK 500 12 LYS A 30 -45.12 -133.99 REMARK 500 12 ASP A 52 32.32 34.83 REMARK 500 12 HIS A 69 49.25 -107.77 REMARK 500 12 SER A 70 163.09 -49.18 REMARK 500 13 GLU A 10 45.04 -79.28 REMARK 500 13 ASP A 13 49.24 -109.62 REMARK 500 13 ALA A 21 125.48 -39.06 REMARK 500 13 LYS A 29 37.35 -95.28 REMARK 500 13 LYS A 30 -49.26 -134.99 REMARK 500 13 SER A 32 48.70 73.62 REMARK 500 13 ASP A 52 41.15 -97.32 REMARK 500 13 LEU A 84 155.40 -45.38 REMARK 500 13 SER A 101 95.47 -65.84 REMARK 500 14 SER A 3 128.10 -174.61 REMARK 500 14 ALA A 21 143.25 -33.26 REMARK 500 14 ASP A 52 45.44 -77.89 REMARK 500 14 SER A 101 120.82 -171.79 REMARK 500 14 SER A 104 41.80 35.86 REMARK 500 15 ALA A 21 140.92 -36.56 REMARK 500 15 PRO A 49 0.21 -69.74 REMARK 500 15 ASP A 52 45.93 -87.12 REMARK 500 15 ARG A 72 -73.47 -71.20 REMARK 500 15 LEU A 84 163.55 -46.74 REMARK 500 16 SER A 5 44.79 -79.31 REMARK 500 16 GLU A 10 42.26 -96.57 REMARK 500 16 LYS A 29 35.01 -95.66 REMARK 500 16 LYS A 30 -52.91 -135.05 REMARK 500 16 ASP A 52 41.47 -103.48 REMARK 500 16 PRO A 103 -179.46 -69.78 REMARK 500 16 SER A 104 42.41 -83.40 REMARK 500 16 SER A 105 151.30 -37.23 REMARK 500 17 SER A 11 101.78 -45.07 REMARK 500 17 ALA A 21 139.57 -34.58 REMARK 500 17 LYS A 29 31.08 -98.38 REMARK 500 17 LYS A 30 -54.90 -130.48 REMARK 500 17 SER A 32 54.15 71.19 REMARK 500 17 ASP A 52 41.92 -101.17 REMARK 500 17 PHE A 61 -37.90 -39.07 REMARK 500 17 SER A 101 103.24 -59.08 REMARK 500 18 ALA A 21 137.52 -33.08 REMARK 500 18 SER A 32 54.93 38.11 REMARK 500 18 PHE A 61 -34.85 -39.52 REMARK 500 18 HIS A 69 45.61 -91.29 REMARK 500 18 SER A 70 150.09 -49.08 REMARK 500 18 LEU A 84 170.83 -45.05 REMARK 500 19 SER A 11 44.22 -80.18 REMARK 500 19 ALA A 21 117.08 -34.22 REMARK 500 19 ARG A 25 -60.15 -103.92 REMARK 500 19 ALA A 26 126.73 -39.10 REMARK 500 19 LYS A 29 32.74 -99.04 REMARK 500 19 LYS A 30 -51.28 -132.66 REMARK 500 19 PHE A 61 -33.74 -37.91 REMARK 500 19 HIS A 69 50.66 -109.52 REMARK 500 19 SER A 70 163.18 -46.57 REMARK 500 19 LEU A 84 153.69 -49.48 REMARK 500 19 LYS A 93 -70.14 -52.70 REMARK 500 19 PRO A 103 6.25 -69.75 REMARK 500 20 ALA A 21 130.09 -38.17 REMARK 500 20 ARG A 25 -60.81 -101.22 REMARK 500 20 ALA A 26 136.77 -34.53 REMARK 500 20 LYS A 30 -52.02 -133.67 REMARK 500 20 ASP A 52 46.97 -76.92 REMARK 500 20 PHE A 61 -32.86 -34.00 REMARK 500 20 PRO A 74 3.21 -69.82 REMARK 500 20 PRO A 103 86.67 -69.77 REMARK 500 20 SER A 105 103.77 -40.89 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 1 ZN A 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 60 ND1 REMARK 620 2 CYS A 28 SG 108.1 REMARK 620 3 CYS A 31 SG 104.2 108.2 REMARK 620 4 CYS A 63 SG 117.8 104.9 113.3 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 ZN ZN A 200 ND1 HIS A 60 1555 1555 2.08 LINK ZN ZN A 200 SG CYS A 28 1555 1555 2.35 LINK ZN ZN A 200 SG CYS A 31 1555 1555 2.34 LINK ZN ZN A 200 SG CYS A 63 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