PDB Short entry for 2N8A HEADER TRANSFERASE 08-OCT-15 2N8A TITLE 1H, 13C AND 15N CHEMICAL SHIFT ASSIGNMENTS AND SOLUTION STRUCTURE FOR TITLE 2 PARP-1 F1F2 DOMAINS IN COMPLEX WITH A DNA SINGLE-STRAND BREAK COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY [ADP-RIBOSE] POLYMERASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-214; COMPND 5 SYNONYM: PARP-1, ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 1, COMPND 6 ARTD1, NAD(+) ADP-RIBOSYLTRANSFERASE 1, ADPRT 1, POLY[ADP-RIBOSE] COMPND 7 SYNTHASE 1; COMPND 8 EC: 2.4.2.30; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (45-MER); COMPND 12 CHAIN: B; COMPND 13 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET13; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 78 AUTHOR D.NEUHAUS,S.EUSTERMANN,J.YANG,W.WU REVDAT 4 19-OCT-16 2N8A 1 REMARK REVDAT 3 05-OCT-16 2N8A 1 TITLE REVDAT 2 23-DEC-15 2N8A 1 JRNL REVDAT 1 02-DEC-15 2N8A 0 JRNL AUTH S.EUSTERMANN,W.F.WU,M.F.LANGELIER,J.C.YANG,L.E.EASTON, JRNL AUTH 2 A.A.RICCIO,J.M.PASCAL,D.NEUHAUS JRNL TITL STRUCTURAL BASIS OF DETECTION AND SIGNALING OF DNA JRNL TITL 2 SINGLE-STRAND BREAKS BY HUMAN PARP-1. JRNL REF MOL.CELL V. 60 742 2015 JRNL REFN ISSN 1097-2765 JRNL PMID 26626479 JRNL DOI 10.1016/J.MOLCEL.2015.10.032 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS CALCULATED USING A REMARK 3 COMBINED NMR/X-RAY PROTOCOL. NMR EVIDENCE ESTABLISHED THE REMARK 3 TOPOLOGY OF THE COMPLEX TO BE A MONOMERIC ASSEMBLY IN WHICH REMARK 3 DOMAIN F1 (PROTEIN RESIDUES 6-91) IS BOUND TO THE DNA STEM WITH REMARK 3 THE 5' TERMINUS AND DOMAIN F2 (PROTEIN RESIDUES 109-200) TO THE REMARK 3 DNA STEM WITH THE 3' TERMINUS; NMR FURTHER SHOWED THAT THE REMARK 3 INDIVIDUAL BINDING MODES OF F1 AND F2 TO THEIR RESPECTIVE STEMS REMARK 3 WAS EQUIVALENT (THOUGH IN A DIFFERENT CONTEXT) TO THOSE SEEN IN REMARK 3 CRYSTAL STRUCTURES PDB 3ODA AND 3ODC RESPECTIVELY. TEMPLATE REMARK 3 STRUCTURES WERE CREATED FROM 3ODA AND 3ODC (AND 1MSY AND 1RNG FOR REMARK 3 THE DNA TETRALOOPS) AND USED TOGETHER WITH NON-CRYSTALLOGRAPHIC REMARK 3 SYMMETRY TERMS IN XPLOR-NIH TO RETAIN THESE FEATURES IN THE REMARK 3 CALCULATED STRUCTURES, WHILE THE RDC AND NOE DERIVED RESTRAINTS REMARK 3 DEFINED THE OVERALL STRUCTURE. FULL DETAILS OF THE APPROACH AND REMARK 3 THE CALCULATION PROTOCOL APPEAR IN THE PRIMARY REFERENCE AND REMARK 3 CORRESPONDING SUPPLEMENTARY MATERIAL FOR THIS ENTRY. REMARK 4 REMARK 4 2N8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-15. REMARK 100 THE RCSB ID CODE IS RCSB104547. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 300; 303 REMARK 210 PH : 7.2; 7.2; 7.2 REMARK 210 IONIC STRENGTH : 0.0004; 0.0004; 0.1 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : SAMPLE 1: 0.2 MM [U-15N; U-13C; REMARK 210 U-2H] PARP-1 1, 0.2 MM DNA (45- REMARK 210 MER), 50 MM [U-2H] TRIS, 1 MM [U- REMARK 210 2H] DTT, 0.1 MM ZNSO4, 95% H2O/5% REMARK 210 D2O; SAMPLE 2: 0.2 MM [U-15N; U- REMARK 210 13C; U-70% 2H] PARP-1 1, 0.2 MM REMARK 210 DNA (45-MER), 50 MM [U-2H] TRIS, REMARK 210 1 MM [U-2H] DTT, 0.1 MM ZNSO4, REMARK 210 95% H2O/5% D2O; SAMPLE 3: 0.2 MM REMARK 210 [U-98% 2H; U-98% 15N] PARP-1 1, REMARK 210 0.2 MM DNA (45-MER), 50 MM [U-2H] REMARK 210 TRIS, 1 MM [U-2H] DTT, 0.1 MM REMARK 210 ZNSO4, 95% H2O/5% D2O; SAMPLE 4A: REMARK 210 0.2 MM PARP-1 1-214, UNIFORM [2H, REMARK 210 15N,13C], BACK-LABELED WITH [1H, REMARK 210 13C] IN THE DELTA-METHYL GROUPS REMARK 210 OF ILE AND ALL METHYL GROUPS OF REMARK 210 LEU AND VAL RESIDUES, USING REMARK 210 SODIUM [4-13C, 3,3-2H2] ALPHA- REMARK 210 KETOBUTYRATE AND SODIUM [3- 2H, REMARK 210 4,4'-13C2] ALPHA-KETOISOVALERATE REMARK 210 AS PRECURSORS TO MAXIMIZE REMARK 210 PROTONATION OF METHYL GROUPS, FOR REMARK 210 USE IN NOE EXPERIMENTS; SODIUM REMARK 210 [3-2H, 4,4'-13C2] ALPHA- REMARK 210 KETOISOVALERATE WAS PREPARED FROM REMARK 210 SODIUM [4,4'-13C2] ALPHA- REMARK 210 KETOISOVALERATE BY EXCHANGE WITH REMARK 210 2H2O AT PH 12.5 AND 45 C FOR 3 REMARK 210 HRS. 0.2 MM DNA (45-MER), 50 MM REMARK 210 [U-2H] TRIS, 1 MM [U-2H] DTT, 0.1 REMARK 210 MM ZNSO4, 95% H2O/5% D2O; SAMPLE REMARK 210 4B: 0.2 MM PARP-1 1-214, UNIFORM REMARK 210 [2H,15N,13C], BACK-LABELED WITH REMARK 210 [1H,13C] IN THE DELTA-METHYL REMARK 210 GROUPS OF ILE AND ALL METHYL REMARK 210 GROUPS OF LEU AND VAL RESIDUES, REMARK 210 USING SODIUM [3,3-2H2,13C4] ALPHA REMARK 210 -KETOBUTYRATE AND SODIUM [3- 2H, REMARK 210 13C5] ALPHA-KETOISOVALERATE AS REMARK 210 PRECURSORS TO PRODUCE LINEAR REMARK 210 CHAINS OF 13C IN THE SIDECHAINS REMARK 210 OF VAL AND LEU, FOR USE IN REMARK 210 ASSIGNMENT EXPERIMENTS TO LINK REMARK 210 METHYL SIGNALS TO C-ALPHA REMARK 210 SIGNALS. 0.2 MM DNA (45-MER), 50 REMARK 210 MM [U-2H] TRIS, 1 MM [U-2H] DTT, REMARK 210 0.1 MM ZNSO4, 100% D2O; SAMPLE 5: REMARK 210 0.2 MM PARP-1 1-214, UNIFORM [2H, REMARK 210 15N,13C], BACK-LABELED WITH [1H, REMARK 210 13C] IN THE METHYL GROUPS OF MET REMARK 210 RESIDUES IN ADDITION TO ILE, LEU REMARK 210 AND VAL METHYL GROUPS AS IN REMARK 210 SAMPLE 4A. 0.2 MM DNA (45-MER), REMARK 210 50 MM [U-2H] TRIS, 1 MM [U-2H] REMARK 210 DTT, 0.1 MM ZNSO4, 100% D2O; REMARK 210 SAMPLE 6: 0.2 MM PARP-1 1-214, REMARK 210 UNIFORM [2H,15N,13C]; BACK- REMARK 210 LABELED WITH [1H,13C] IN THE REMARK 210 METHYL GROUPS OF ILE, LEU AND VAL REMARK 210 METHYL GROUPS AS IN SAMPLE 4A AND REMARK 210 [1H,13C,15N] PHE RESIDUES. 0.2 MM REMARK 210 DNA (45-MER), 50 MM [U-2H] TRIS, REMARK 210 1 MM [U-2H] DTT, 0.1 MM ZNSO4, REMARK 210 100% D2O; SAMPLE 7: 0.2 MM PARP-1 REMARK 210 1-214, SORTASE LIGATED, BLOCK- REMARK 210 LABELLED SAMPLE. (N.B. RESIDUES REMARK 210 103 AND 104 OF WT SEQUENCE REMARK 210 DELETED, ADDITIONAL RESIDUES REMARK 210 LPETGGG INSERTED BETWEEN RESIDUES REMARK 210 102 AND 105; THIS SAMPLE WAS NOT REMARK 210 USED FOR MAKING ANY ASSIGNMENTS REMARK 210 OF RESIDUES IN THIS REGION, WHICH REMARK 210 IS IN THE FLEXIBLE LINKER BETWEEN REMARK 210 DOMAINS). LABELLING FOR RESIDUES REMARK 210 1-102 (AND LPET OF INSERTION): REMARK 210 UNIFORM [1H,12C,15N]. LABELLING REMARK 210 FOR RESIDUES 105-214 (AND GGG OF REMARK 210 INSERTION): [2H,15N,13C] BACK- REMARK 210 LABELED WITH [1H,13C] ILE, LEU REMARK 210 VAL AND MET METHYL GROUPS LABELED REMARK 210 AS IN SAMPLE 5. 0.2 MM DNA (45- REMARK 210 MER), 50 MM [U-2H] TRIS, 1 MM [U- REMARK 210 2H] DTT, 0.1 MM ZNSO4, 100% D2O; REMARK 210 SAMPLE 8: 0.2 MM PARP-1 1-214, REMARK 210 SORTASE LIGATED, BLOCK-LABELLED REMARK 210 SAMPLE. (N.B. RESIDUES 103 AND REMARK 210 104 OF WT SEQUENCE DELETED, REMARK 210 ADDITIONAL RESIDUES LPETGGG REMARK 210 INSERTED BETWEEN RESIDUES 102 AND REMARK 210 105; THIS SAMPLE WAS NOT USED FOR REMARK 210 MAKING ANY ASSIGNMENTS OF REMARK 210 RESIDUES IN THIS REGION, WHICH IS REMARK 210 IN THE FLEXIBLE LINKER BETWEEN REMARK 210 DOMAINS). LABELLING FOR RESIDUES REMARK 210 1-102 (AND LPET OF INSERTION): REMARK 210 UNIFORM [1H,12C,15N]. LABELLING REMARK 210 FOR RESIDUES 105-214 (AND GGG OF REMARK 210 INSERTION): [2H,15N,13C] BACK REMARK 210 LABELED WITH [1H,13C] MET METHYL REMARK 210 GROUPS AS IN SAMPLE 5 AND [13C, REMARK 210 15N,1H] ARG RESIDUES. 0.2 MM DNA REMARK 210 (45-MER), 50 MM [U-2H] TRIS, 1 MM REMARK 210 [U-2H] DTT, 0.1 MM ZNSO4, 100% REMARK 210 D2O; SAMPLE 9: 0.2 MM PARP-1 1- REMARK 210 214, SORTASE LIGATED, BLOCK- REMARK 210 LABELLED SAMPLE. (N.B. RESIDUES REMARK 210 103 AND 104 OF WT SEQUENCE REMARK 210 DELETED, ADDITIONAL RESIDUES REMARK 210 LPETGGG INSERTED BETWEEN RESIDUES REMARK 210 102 AND 105; THIS SAMPLE WAS NOT REMARK 210 USED FOR MAKING ANY ASSIGNMENTS REMARK 210 OF RESIDUES IN THIS REGION, WHICH REMARK 210 IS IN THE FLEXIBLE LINKER BETWEEN REMARK 210 DOMAINS). LABELLING FOR RESIDUES REMARK 210 1-102 (AND LPET OF INSERTION): REMARK 210 [2H,15N,13C] BACK-LABELED WITH REMARK 210 ILE, LEU AND VAL METHYL GROUPS REMARK 210 LABELED AS IN SAMPLE 4A AND [1H, REMARK 210 13C,15N] ARG RESIDUES. LABELLING REMARK 210 FOR RESIDUES 105-214 (AND GGG OF REMARK 210 INSERTION): UNIFORM [1H,12C,15N]. REMARK 210 0.2 MM DNA (45-MER), 50 MM [U-2H] REMARK 210 TRIS, 1 MM [U-2H] DTT, 0.1 MM REMARK 210 ZNSO4, 95% H2O/5% D2O; SAMPLE 10: REMARK 210 0.2 MM PARP-1 1-214, SORTASE REMARK 210 LIGATED, BLOCK-LABELLED SAMPLE. REMARK 210 (N.B. RESIDUES 103 AND 104 OF WT REMARK 210 SEQUENCE DELETED, ADDITIONAL REMARK 210 RESIDUES LPETGGG INSERTED BETWEEN REMARK 210 RESIDUES 102 AND 105; THIS SAMPLE REMARK 210 WAS NOT USED FOR MAKING ANY REMARK 210 ASSIGNMENTS OF RESIDUES IN THIS REMARK 210 REGION, WHICH IS IN THE FLEXIBLE REMARK 210 LINKER BETWEEN DOMAINS). REMARK 210 LABELLING FOR RESIDUES 1-102 (AND REMARK 210 LPET OF INSERTION): [2H,15N,13C] REMARK 210 BACK-LABELED WITH ILE, LEU AND REMARK 210 VAL METHYL GROUPS LABELED AS IN REMARK 210 SAMPLE 4A AND [1H,13C,15N] PHE REMARK 210 RESIDUES. LABELLING FOR RESIDUES REMARK 210 105-214 (AND GGG OF INSERTION): REMARK 210 UNIFORM [1H,12C,15N]. 0.2 MM DNA REMARK 210 (45-MER), 50 MM [U-2H] TRIS, 1 MM REMARK 210 [U-2H] DTT, 0.1 MM ZNSO4, 100% REMARK 210 D2O; SAMPLE 11: 0.2 MM SEE SAMPLE REMARK 210 DETAILS SECTION PARP-1 1, 0.2 MM REMARK 210 DNA (45-MER), 50 MM [U-2H] TRIS, REMARK 210 1 MM [U-2H] DTT, 0.1 MM ZNSO4, REMARK 210 100% D2O; SAMPLE 12: 0.2 MM DNA REMARK 210 (45-MER), 50 MM [U-2H] TRIS, 1 MM REMARK 210 [U-2H] DTT, 0.1 MM ZNSO4, 100% REMARK 210 D2O; SAMPLE 13: 0.2 MM DNA (45- REMARK 210 MER), 50 MM [U-2H] TRIS, 1 MM [U- REMARK 210 2H] DTT, 0.1 MM ZNSO4, 95% H2O/5% REMARK 210 D2O; SAMPLE 14: 0.2 MM [U-15N; U- REMARK 210 13C; U-2H] PARP-1 1, 0.2 MM DNA REMARK 210 (45-MER), 50 MM [U-2H] TRIS, 1 MM REMARK 210 [U-2H] DTT, 0.1 MM ZNSO4, 100% REMARK 210 D2O; SAMPLE 15: 0.2 MM [U-15N; U- REMARK 210 13C; U-2H] PARP-1 1, 50 MM [U-2H] REMARK 210 TRIS, 1 MM [U-2H] DTT, 0.1 UM REMARK 210 ZNSO4, 200 MM SODIUM CHLORIDE, REMARK 210 95% H2O/5% D2O; SAMPLE 16: 0.2 MM REMARK 210 [U-15N; U-13C; U-2H] PARP-1 1, REMARK 210 0.2 MM DNA (45-MER), 50 MM [U-2H] REMARK 210 TRIS, 1 MM [U-2H] DTT, 0.1 UM REMARK 210 ZNSO4, 200 MM SODIUM CHLORIDE, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N TROSY; 2D 1H-13C HMQC; REMARK 210 TROSY-NHCACB (OPTIMIZED FOR CB); REMARK 210 TROSY-HNCA; TROSY-HN(CO)CA; 3D 1H REMARK 210 -13C-1H NOESY-HMQC; HMCM(CG)CBCA; REMARK 210 2D 1H-1H NOESY; 3D 13C-13C-1H REMARK 210 HMQC-NOESY-HMQC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-1H NOESY FILTERED REMARK 210 TO ACCEPT 13C-1H IN W2; 2D 1H-1H REMARK 210 NOESY FILTERED TO ACCEPT 13C-1H REMARK 210 IN W2 (NO DECOUPLING IN W1); 2D REMARK 210 1H-13C HSQC ALIPHATIC; 2D 1H-1H REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE I; AVANCE II+; DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR_NIH 2.28, SPARKY 3.115, REMARK 210 TOPSPIN 2.1, ANALYSIS 2.4.1, REMARK 210 NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 78 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 78 REMARK 210 CONFORMERS, SELECTION CRITERIA : TOTAL, TENSOR AND NOE XPLOR REMARK 210 ENERGIES SIMULTANEOUSLY BELOW REMARK 210 THRESHOLDS (6000, 1500 AND 2 REMARK 210 KCAL.MOL-1 RESPECTIVELY) REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SAMPLE NUMBERS USED HERE CORRESPOND TO THOSE USED IN THE REMARK 210 SUPPLEMENTARY MATERIAL FOR THE PRIMARY CITATION 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 300 REMARK: THE ASSEMBLY IS A HETERO-DIMER MADE OF ONE CHAIN OF POLY REMARK 300 [ADP-RIBOSE] POLYMERASE 1 AND ONE CHAIN OF DNA (45-MER). 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 O2 DC B 33 H22 DG B 36 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 13 DG B 21 C2 DG B 21 N2 0.060 REMARK 500 15 LYS A 22 CA LYS A 22 CB 0.173 REMARK 500 36 SER A 20 CA SER A 20 CB -0.112 REMARK 500 44 SER A 27 CA SER A 27 CB 0.091 REMARK 500 55 DA B 15 N9 DA B 15 C4 -0.037 REMARK 500 59 DG B 39 O3' DG B 39 C3' -0.043 REMARK 500 64 DC B 2 O3' DC B 2 C3' -0.037 REMARK 500 72 SER A 25 CA SER A 25 CB -0.102 REMARK 500 75 SER A 27 CA SER A 27 CB -0.105 REMARK 500 75 DG B 21 C2' DG B 21 C1' 0.065 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 5 SER A 20 N - CA - CB ANGL. DEV. = -9.6 DEGREES REMARK 500 5 LYS A 22 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 10 SER A 185 N - CA - CB ANGL. DEV. = -9.4 DEGREES REMARK 500 12 DG B 4 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 13 DG B 21 N1 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 14 DC B 22 C5' - C4' - C3' ANGL. DEV. = 7.3 DEGREES REMARK 500 15 CYS A 24 N - CA - CB ANGL. DEV. = -17.9 DEGREES REMARK 500 23 LYS A 22 N - CA - CB ANGL. DEV. = -12.2 DEGREES REMARK 500 26 HIS A 50 CA - CB - CG ANGL. DEV. = -10.6 DEGREES REMARK 500 36 CYS A 24 N - CA - CB ANGL. DEV. = -13.9 DEGREES REMARK 500 40 SER A 20 N - CA - CB ANGL. DEV. = -13.6 DEGREES REMARK 500 40 LYS A 22 N - CA - CB ANGL. DEV. = -12.4 DEGREES REMARK 500 42 SER A 20 CB - CA - C ANGL. DEV. = 13.4 DEGREES REMARK 500 42 SER A 20 N - CA - CB ANGL. DEV. = -16.5 DEGREES REMARK 500 42 DC B 22 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES REMARK 500 43 DA B 40 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 48 LYS A 22 CA - CB - CG ANGL. DEV. = -15.0 DEGREES REMARK 500 55 LYS A 182 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 55 DA B 15 O3' - P - OP2 ANGL. DEV. = 7.3 DEGREES REMARK 500 59 DA B 40 O5' - P - OP1 ANGL. DEV. = 7.5 DEGREES REMARK 500 67 DC B 41 O5' - P - OP1 ANGL. DEV. = 8.6 DEGREES REMARK 500 67 DC B 41 O5' - P - OP2 ANGL. DEV. = -5.4 DEGREES REMARK 500 72 SER A 25 N - CA - CB ANGL. DEV. = -15.3 DEGREES REMARK 500 75 DG B 21 O4' - C1' - N9 ANGL. DEV. = 1.8 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 1 GLU A 3 178.20 54.54 REMARK 500 1 SER A 5 19.36 -143.83 REMARK 500 1 SER A 25 -10.05 73.23 REMARK 500 1 ASP A 31 -9.81 74.34 REMARK 500 1 VAL A 94 103.75 54.94 REMARK 500 1 THR A 95 96.22 -53.19 REMARK 500 1 LYS A 97 -164.75 -168.81 REMARK 500 1 GLN A 99 -48.69 -163.92 REMARK 500 1 LYS A 105 -177.52 53.26 REMARK 500 1 LYS A 108 30.69 -145.79 REMARK 500 1 MET A 129 13.23 59.33 REMARK 500 1 ARG A 173 158.25 -46.20 REMARK 500 1 LYS A 207 -65.53 -95.76 REMARK 500 1 LYS A 209 48.33 -154.33 REMARK 500 1 VAL A 213 49.31 -155.29 REMARK 500 2 SER A 25 -10.12 73.43 REMARK 500 2 ASP A 31 -9.95 74.41 REMARK 500 2 THR A 95 -40.03 -138.87 REMARK 500 2 SER A 104 73.93 -100.87 REMARK 500 2 ALA A 106 -72.72 -164.80 REMARK 500 2 MET A 129 13.08 59.48 REMARK 500 2 MET A 153 108.73 -59.30 REMARK 500 2 ARG A 173 158.29 -46.22 REMARK 500 2 LYS A 203 -162.70 -124.62 REMARK 500 2 SER A 204 92.10 -69.59 REMARK 500 2 ARG A 208 56.31 -155.92 REMARK 500 2 LYS A 209 -161.07 -117.64 REMARK 500 2 VAL A 213 27.72 -147.70 REMARK 500 3 GLU A 3 -51.99 -121.06 REMARK 500 3 SER A 4 -74.21 -165.42 REMARK 500 3 SER A 25 -10.14 73.44 REMARK 500 3 ASP A 31 -10.05 74.48 REMARK 500 3 THR A 95 77.51 -103.38 REMARK 500 3 SER A 104 75.93 -161.22 REMARK 500 3 GLU A 107 -37.63 -170.84 REMARK 500 3 MET A 129 13.10 59.42 REMARK 500 3 ARG A 173 158.26 -46.16 REMARK 500 3 GLU A 205 -62.45 -92.00 REMARK 500 3 LYS A 209 -52.90 -152.08 REMARK 500 4 SER A 25 -10.02 73.34 REMARK 500 4 ASP A 31 -9.77 74.27 REMARK 500 4 VAL A 94 55.58 -145.36 REMARK 500 4 GLN A 99 92.69 51.87 REMARK 500 4 ASP A 100 64.25 -107.84 REMARK 500 4 ILE A 102 -39.03 -169.22 REMARK 500 4 SER A 104 -179.57 -172.28 REMARK 500 4 LYS A 108 34.11 -168.88 REMARK 500 4 MET A 129 13.35 59.29 REMARK 500 4 ARG A 173 158.25 -46.25 REMARK 500 4 LYS A 203 118.89 -160.63 REMARK 500 REMARK 500 THIS ENTRY HAS 994 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 DC B 2 0.10 SIDE CHAIN REMARK 500 2 DT B 3 0.10 SIDE CHAIN REMARK 500 7 DC B 24 0.08 SIDE CHAIN REMARK 500 30 DC B 24 0.10 SIDE CHAIN REMARK 500 38 DC B 24 0.09 SIDE CHAIN REMARK 500 42 DG B 1 0.07 SIDE CHAIN REMARK 500 45 DC B 24 0.10 SIDE CHAIN REMARK 500 55 DA B 13 0.08 SIDE CHAIN REMARK 500 55 DC B 42 0.09 SIDE CHAIN REMARK 500 71 DG B 1 0.06 SIDE CHAIN 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 A1000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 ND1 REMARK 620 2 CYS A 21 SG 100.6 REMARK 620 3 CYS A 56 SG 117.0 107.0 REMARK 620 4 CYS A 24 SG 107.2 104.2 118.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 159 ND1 REMARK 620 2 CYS A 125 SG 97.3 REMARK 620 3 CYS A 162 SG 115.6 109.1 REMARK 620 4 CYS A 128 SG 112.1 101.3 118.1 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 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25888 RELATED DB: BMRB REMARK 900 RELATED ID: 25889 RELATED DB: BMRB REMARK 900 RELATED ID: 25890 RELATED DB: BMRB REMARK 900 RELATED ID: 25891 RELATED DB: BMRB REMARK 900 RELATED ID: 25892 RELATED DB: BMRB REMARK 900 RELATED ID: 25893 RELATED DB: BMRB REMARK 900 RELATED ID: 25894 RELATED DB: BMRB REMARK 900 RELATED ID: 25895 RELATED DB: BMRB DBREF 2N8A A 1 214 UNP P09874 PARP1_HUMAN 1 214 DBREF 2N8A B 1 45 PDB 2N8A 2N8A 1 45 SEQRES 1 A 214 MET ALA GLU SER SER ASP LYS LEU TYR ARG VAL GLU TYR SEQRES 2 A 214 ALA LYS SER GLY ARG ALA SER CYS LYS LYS CYS SER GLU SEQRES 3 A 214 SER ILE PRO LYS ASP SER LEU ARG MET ALA ILE MET VAL SEQRES 4 A 214 GLN SER PRO MET PHE ASP GLY LYS VAL PRO HIS TRP TYR SEQRES 5 A 214 HIS PHE SER CYS PHE TRP LYS VAL GLY HIS SER ILE ARG SEQRES 6 A 214 HIS PRO ASP VAL GLU VAL ASP GLY PHE SER GLU LEU ARG SEQRES 7 A 214 TRP ASP ASP GLN GLN LYS VAL LYS LYS THR ALA GLU ALA SEQRES 8 A 214 GLY GLY VAL THR GLY LYS GLY GLN ASP GLY ILE GLY SER SEQRES 9 A 214 LYS ALA GLU LYS THR LEU GLY ASP PHE ALA ALA GLU TYR SEQRES 10 A 214 ALA LYS SER ASN ARG SER THR CYS LYS GLY CYS MET GLU SEQRES 11 A 214 LYS ILE GLU LYS GLY GLN VAL ARG LEU SER LYS LYS MET SEQRES 12 A 214 VAL ASP PRO GLU LYS PRO GLN LEU GLY MET ILE ASP ARG SEQRES 13 A 214 TRP TYR HIS PRO GLY CYS PHE VAL LYS ASN ARG GLU GLU SEQRES 14 A 214 LEU GLY PHE ARG PRO GLU TYR SER ALA SER GLN LEU LYS SEQRES 15 A 214 GLY PHE SER LEU LEU ALA THR GLU ASP LYS GLU ALA LEU SEQRES 16 A 214 LYS LYS GLN LEU PRO GLY VAL LYS SER GLU GLY LYS ARG SEQRES 17 A 214 LYS GLY ASP GLU VAL ASP SEQRES 1 B 45 DG DC DT DG DG DC DT DT DC DG DT DA DA SEQRES 2 B 45 DG DA DA DG DC DC DA DG DC DT DC DG DC SEQRES 3 B 45 DG DG DT DC DA DG DC DT DT DG DC DT DG SEQRES 4 B 45 DA DC DC DG DC DG HET ZN A1000 1 HET ZN A1001 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 1 PHE A 54 VAL A 60 1 7 HELIX 2 2 HIS A 66 GLU A 70 1 5 HELIX 3 3 GLY A 73 LEU A 77 5 5 HELIX 4 4 ARG A 78 ALA A 91 1 14 HELIX 5 5 HIS A 159 ASN A 166 1 8 HELIX 6 6 SER A 177 LEU A 181 5 5 HELIX 7 7 GLY A 183 LEU A 187 5 5 HELIX 8 8 ALA A 188 LEU A 199 1 12 SHEET 1 A 4 LYS A 47 HIS A 53 0 SHEET 2 A 4 LEU A 33 GLN A 40 -1 N VAL A 39 O VAL A 48 SHEET 3 A 4 TYR A 9 TYR A 13 -1 N GLU A 12 O ARG A 34 SHEET 4 A 4 VAL A 71 ASP A 72 1 O ASP A 72 N TYR A 9 SHEET 1 B 3 PHE A 113 TYR A 117 0 SHEET 2 B 3 VAL A 137 LYS A 141 -1 O ARG A 138 N GLU A 116 SHEET 3 B 3 TRP A 157 TYR A 158 -1 O TYR A 158 N LEU A 139 SHEET 1 C 2 MET A 143 VAL A 144 0 SHEET 2 C 2 MET A 153 ILE A 154 -1 O ILE A 154 N MET A 143 LINK ND1 HIS A 53 ZN ZN A1000 1555 1555 2.01 LINK ND1 HIS A 159 ZN ZN A1001 1555 1555 2.01 LINK SG CYS A 125 ZN ZN A1001 1555 1555 2.28 LINK SG CYS A 21 ZN ZN A1000 1555 1555 2.28 LINK SG CYS A 56 ZN ZN A1000 1555 1555 2.31 LINK SG CYS A 24 ZN ZN A1000 1555 1555 2.31 LINK SG CYS A 162 ZN ZN A1001 1555 1555 2.31 LINK SG CYS A 128 ZN ZN A1001 1555 1555 2.31 SITE 1 AC1 4 CYS A 21 CYS A 24 HIS A 53 CYS A 56 SITE 1 AC2 4 CYS A 125 CYS A 128 HIS A 159 CYS A 162 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