HEADER TRANSFERASE 24-SEP-07 2JVN TITLE DOMAIN C OF HUMAN PARP-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY [ADP-RIBOSE] POLYMERASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 233-358; COMPND 5 SYNONYM: PARP-1, ADPRT, NAD+, ADP-RIBOSYLTRANSFERASE 1, POLY[ADP- COMPND 6 RIBOSE] SYNTHETASE 1; COMPND 7 EC: 2.4.2.30; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PARP1, ADPRT, PPOL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET KEYWDS PROTEIN, PARP, ADP-RIBOSYLATION, DNA DAMAGE, DNA REPAIR, DNA-BINDING, KEYWDS 2 GLYCOSYLTRANSFERASE, METAL-BINDING, NAD, NUCLEUS, PHOSPHORYLATION, KEYWDS 3 TRANSFERASE, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.HOFFMAN,Z.TAO,H.LIU REVDAT 5 01-MAY-24 2JVN 1 REMARK REVDAT 4 01-MAY-13 2JVN 1 MODEL VERSN REVDAT 3 24-FEB-09 2JVN 1 VERSN REVDAT 2 17-JUN-08 2JVN 1 JRNL REVDAT 1 13-MAY-08 2JVN 0 JRNL AUTH Z.TAO,P.GAO,D.W.HOFFMAN,H.W.LIU JRNL TITL DOMAIN C OF HUMAN POLY(ADP-RIBOSE) POLYMERASE-1 IS IMPORTANT JRNL TITL 2 FOR ENZYME ACTIVITY AND CONTAINS A NOVEL ZINC-RIBBON MOTIF. JRNL REF BIOCHEMISTRY V. 47 5804 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18452307 JRNL DOI 10.1021/BI800018A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JVN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000100347. 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 : 260 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 13C; U-100% 15N] REMARK 210 PARP, 250 MM SODIUM CHLORIDE, 10 REMARK 210 MM POTASSIUM PHOSPHATE, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: CLOSE CONTACTS 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 HB3 CYS A 298 HB3 CYS A 321 1.26 REMARK 500 O GLY A 275 H ALA A 278 1.35 REMARK 500 O SER A 257 H LEU A 261 1.46 REMARK 500 O GLY A 275 N ALA A 278 1.99 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 1 SER A 274 27.66 -79.04 REMARK 500 1 PRO A 294 156.82 -44.94 REMARK 500 1 ALA A 308 105.82 -169.82 REMARK 500 1 TRP A 318 20.64 -147.52 REMARK 500 1 PRO A 336 179.50 -51.94 REMARK 500 1 SER A 343 -25.10 -142.53 REMARK 500 1 LEU A 348 -71.75 -62.17 REMARK 500 1 ILE A 356 25.80 -60.10 REMARK 500 2 SER A 274 27.41 -76.47 REMARK 500 2 GLU A 276 -43.68 -28.61 REMARK 500 2 ALA A 308 105.86 -170.16 REMARK 500 2 TRP A 318 23.20 -150.51 REMARK 500 2 PRO A 336 -178.01 -44.43 REMARK 500 2 SER A 343 -34.48 -139.12 REMARK 500 2 LEU A 348 -88.70 -61.48 REMARK 500 2 LYS A 352 94.22 -48.83 REMARK 500 2 ILE A 356 66.73 -61.73 REMARK 500 3 SER A 274 26.26 -77.59 REMARK 500 3 GLU A 276 -40.55 -29.83 REMARK 500 3 PRO A 294 152.43 -45.60 REMARK 500 3 ALA A 308 105.89 -170.74 REMARK 500 3 TRP A 318 25.75 -154.88 REMARK 500 3 PRO A 336 171.89 -40.40 REMARK 500 3 GLU A 341 -73.70 -53.68 REMARK 500 3 SER A 343 -9.89 83.51 REMARK 500 3 LYS A 352 96.99 -46.59 REMARK 500 4 SER A 274 27.82 -77.79 REMARK 500 4 PRO A 294 152.30 -44.12 REMARK 500 4 ALA A 308 106.32 -171.81 REMARK 500 4 TRP A 318 25.15 -154.40 REMARK 500 4 PRO A 336 -177.45 -47.17 REMARK 500 4 SER A 343 -25.49 -144.63 REMARK 500 4 LEU A 348 -85.06 -62.23 REMARK 500 4 LYS A 352 93.65 -49.74 REMARK 500 4 ILE A 356 69.92 -35.05 REMARK 500 5 PRO A 294 159.60 -44.44 REMARK 500 5 ALA A 308 106.54 -170.71 REMARK 500 5 TRP A 318 25.39 -154.90 REMARK 500 5 GLN A 326 -73.34 -40.89 REMARK 500 5 PRO A 328 171.65 -57.08 REMARK 500 5 PRO A 336 -178.23 -43.60 REMARK 500 5 SER A 343 -31.98 166.00 REMARK 500 5 LYS A 352 93.69 -50.39 REMARK 500 5 ILE A 356 18.03 -60.17 REMARK 500 6 SER A 274 27.92 -78.53 REMARK 500 6 GLU A 276 -45.07 -28.68 REMARK 500 6 PRO A 294 150.52 -44.47 REMARK 500 6 ALA A 308 106.35 -170.85 REMARK 500 6 TRP A 318 25.37 -154.95 REMARK 500 6 GLN A 326 -74.62 -39.97 REMARK 500 REMARK 500 THIS ENTRY HAS 92 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 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 295 SG REMARK 620 2 CYS A 298 SG 107.8 REMARK 620 3 CYS A 311 SG 108.7 115.5 REMARK 620 4 CYS A 321 SG 109.1 107.2 108.4 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 400 DBREF 2JVN A 233 358 UNP P09874 PARP1_HUMAN 233 358 SEQRES 1 A 126 LYS LEU GLU LYS ALA LEU LYS ALA GLN ASN ASP LEU ILE SEQRES 2 A 126 TRP ASN ILE LYS ASP GLU LEU LYS LYS VAL CYS SER THR SEQRES 3 A 126 ASN ASP LEU LYS GLU LEU LEU ILE PHE ASN LYS GLN GLN SEQRES 4 A 126 VAL PRO SER GLY GLU SER ALA ILE LEU ASP ARG VAL ALA SEQRES 5 A 126 ASP GLY MET VAL PHE GLY ALA LEU LEU PRO CYS GLU GLU SEQRES 6 A 126 CYS SER GLY GLN LEU VAL PHE LYS SER ASP ALA TYR TYR SEQRES 7 A 126 CYS THR GLY ASP VAL THR ALA TRP THR LYS CYS MET VAL SEQRES 8 A 126 LYS THR GLN THR PRO ASN ARG LYS GLU TRP VAL THR PRO SEQRES 9 A 126 LYS GLU PHE ARG GLU ILE SER TYR LEU LYS LYS LEU LYS SEQRES 10 A 126 VAL LYS LYS GLN ASP ARG ILE PHE PRO HET ZN A 400 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 LYS A 233 CYS A 256 1 24 HELIX 2 2 SER A 257 ASN A 268 1 12 HELIX 3 3 GLY A 275 GLY A 290 1 16 HELIX 4 4 GLU A 338 ILE A 342 5 5 HELIX 5 5 SER A 343 LYS A 349 1 7 SHEET 1 A 2 ALA A 291 LEU A 292 0 SHEET 2 A 2 ARG A 330 LYS A 331 -1 O LYS A 331 N ALA A 291 SHEET 1 B 3 GLY A 300 LYS A 305 0 SHEET 2 B 3 ALA A 308 THR A 316 -1 O TYR A 310 N VAL A 303 SHEET 3 B 3 THR A 319 THR A 325 -1 O THR A 319 N THR A 316 LINK SG CYS A 295 ZN ZN A 400 1555 1555 2.35 LINK SG CYS A 298 ZN ZN A 400 1555 1555 2.27 LINK SG CYS A 311 ZN ZN A 400 1555 1555 2.23 LINK SG CYS A 321 ZN ZN A 400 1555 1555 2.33 SITE 1 AC1 2 CYS A 295 GLU A 297 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