HEADER LYASE 04-NOV-09 2KQC TITLE SECOND PBZ DOMAIN OF HUMAN APLF PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: APRATAXIN AND PNK-LIKE FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 368-451, PBZ-TYPE 2 DOMAIN; COMPND 5 SYNONYM: APURINIC-APYRIMIDINIC ENDONUCLEASE APLF, PNK AND APTX-LIKE COMPND 6 FHA DOMAIN-CONTAINING PROTEIN, XRCC1-INTERACTING PROTEIN 1; COMPND 7 EC: 4.2.99.18; 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: APLF, C2ORF13, PALF, XIP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-1 KEYWDS ADP-RIBOSYLATION, DNA DAMAGE, DNA REPAIR, METAL-BINDING, NUCLEOTIDE- KEYWDS 2 BINDING, NUCLEUS, ZINC, ZINC-FINGER, LYASE EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR D.NEUHAUS,S.EUSTERMANN,C.BROCKMANN,J.YANG REVDAT 3 16-MAR-22 2KQC 1 REMARK SEQADV LINK REVDAT 2 16-FEB-10 2KQC 1 JRNL REVDAT 1 19-JAN-10 2KQC 0 JRNL AUTH S.EUSTERMANN,C.BROCKMANN,P.V.MEHROTRA,J.C.YANG,D.LOAKES, JRNL AUTH 2 S.C.WEST,I.AHEL,D.NEUHAUS JRNL TITL SOLUTION STRUCTURES OF THE TWO PBZ DOMAINS FROM HUMAN APLF JRNL TITL 2 AND THEIR INTERACTION WITH POLY(ADP-RIBOSE). JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 241 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20098424 JRNL DOI 10.1038/NSMB.1747 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH, XPLOR-NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (XPLOR REMARK 3 -NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KQC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000101441. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.4 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM POTASSIUM PYROPHOSPHATE, REMARK 210 200 MM SODIUM CHLORIDE, 100 UM REMARK 210 ZINC SULPHATE, 2 MM [U-2H] DTT, REMARK 210 0.5-0.6 MM [U-98% 13C; U-98% 15N] REMARK 210 APLF_363-451, 95% H2O/5% D2O; REMARK 210 20 MM POTASSIUM PYROPHOSPHATE, REMARK 210 200 MM SODIUM CHLORIDE, 100 UM REMARK 210 ZINC SULPHATE, 2 MM [U-2H] DTT, REMARK 210 0.5-0.6 MM [U-98% 13C; U-98% 15N] REMARK 210 APLF_363-451, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N HMQC REMARK 210 LONG-RANGE; 2D 1H-13C HSQC FULL- REMARK 210 WIDTH; 2D 1H-13C HSQC ALIPHATIC; REMARK 210 2D 1H-13C HSQC AROMATIC; 2D 1H- REMARK 210 1H NOESY; 2D 1H-1H NOESY REMARK 210 FILTERED; 3D CBCANH; 3D CBCA(CO) REMARK 210 NH; 3D HBHANH; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 3D HNHB; 3D HACAHB- REMARK 210 COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 THE AUTHOR STATES THAT NMR WAS CARRIED OUT ON A SINGLE FRAGMENT REMARK 210 (363-451) REMARK 210 CONTAINING BOTH FINGERS F1 AND F2 OF APLF, BUT THE STRUCTURE REMARK 210 CALCULATIONS REMARK 210 WERE CARRIED OUT SEPARATELY FOR EACH FINGER. THIS CO-ORDINATE REMARK 210 FILE INCLUDES REMARK 210 RESIDUES 405-451 AND CONTAINS F2 AS WELL AS THE UNSTRUCTURED REMARK 210 REGIONS ON REMARK 210 EITHER SIDE. 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 400 REMARK 400 COMPOUND REMARK 400 RESIDUES 363-404 ARE NOT SHOWN IN THE COORDINATES BECAUSE STRUCTURE REMARK 400 CALCULATIONS WERE CARRIED OUT ON RESIDUES 405-451 ONLY. 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 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 VAL A 407 54.54 -111.45 REMARK 500 1 ILE A 409 51.67 -115.09 REMARK 500 1 VAL A 410 75.07 -108.86 REMARK 500 1 ASP A 413 44.58 -169.91 REMARK 500 1 PRO A 419 -71.12 -85.87 REMARK 500 1 GLU A 420 108.23 167.58 REMARK 500 1 SER A 426 50.40 -99.73 REMARK 500 1 ASN A 441 -159.03 -173.62 REMARK 500 1 THR A 442 55.22 -151.37 REMARK 500 1 ARG A 446 -43.26 179.26 REMARK 500 1 LEU A 449 -50.32 -179.67 REMARK 500 1 ASP A 450 98.09 54.10 REMARK 500 2 VAL A 407 57.86 -107.21 REMARK 500 2 ILE A 409 71.34 -116.60 REMARK 500 2 PRO A 419 -78.31 -77.88 REMARK 500 2 GLU A 420 108.08 165.71 REMARK 500 2 SER A 426 51.01 -98.24 REMARK 500 2 HIS A 440 39.05 -144.05 REMARK 500 2 THR A 442 74.11 58.66 REMARK 500 2 ARG A 446 -43.91 179.41 REMARK 500 2 ASN A 447 79.93 -111.59 REMARK 500 2 ASP A 450 85.58 51.05 REMARK 500 3 ILE A 409 54.17 -118.08 REMARK 500 3 ASP A 413 38.69 -159.84 REMARK 500 3 THR A 415 65.66 -115.04 REMARK 500 3 PRO A 419 -87.80 -77.70 REMARK 500 3 GLU A 420 108.26 174.21 REMARK 500 3 SER A 426 49.48 -78.59 REMARK 500 3 THR A 442 79.46 58.76 REMARK 500 3 ASP A 450 78.35 51.51 REMARK 500 4 VAL A 410 64.62 -101.77 REMARK 500 4 GLU A 414 41.25 -160.98 REMARK 500 4 THR A 415 61.74 -101.95 REMARK 500 4 PRO A 419 -82.06 -79.82 REMARK 500 4 GLU A 420 104.27 171.55 REMARK 500 4 SER A 426 49.40 -97.69 REMARK 500 4 ASN A 441 -155.39 -173.15 REMARK 500 4 THR A 442 40.79 -162.56 REMARK 500 4 ARG A 446 -51.71 -169.78 REMARK 500 5 ILE A 409 56.01 -111.20 REMARK 500 5 VAL A 410 79.30 -107.72 REMARK 500 5 GLU A 414 40.19 -159.17 REMARK 500 5 THR A 415 68.38 -104.12 REMARK 500 5 PRO A 419 -73.62 -82.49 REMARK 500 5 GLU A 420 112.17 162.93 REMARK 500 5 SER A 426 48.31 -97.45 REMARK 500 5 ARG A 439 -167.92 -102.81 REMARK 500 5 HIS A 440 57.89 -154.04 REMARK 500 5 ASN A 441 -33.93 163.24 REMARK 500 5 VAL A 445 51.29 -143.44 REMARK 500 REMARK 500 THIS ENTRY HAS 261 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 421 SG REMARK 620 2 CYS A 427 SG 116.2 REMARK 620 3 HIS A 434 NE2 103.9 114.6 REMARK 620 4 HIS A 440 NE2 103.8 107.4 110.3 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR 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 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16596 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFTS FOR THIS SYSTEM REMARK 900 RELATED ID: 2KQB RELATED DB: PDB REMARK 900 FIRST PBZ DOMAIN OF HUMAN APLF PROTEIN REMARK 900 RELATED ID: 2KQD RELATED DB: PDB REMARK 900 FIRST PBZ DOMAIN OF HUMAN APLF PROTEIN IN COMPLEX WITH REMARK 900 RIBOFURANOSYLADENOSINE REMARK 900 RELATED ID: 2KQE RELATED DB: PDB REMARK 900 SECOND PBZ DOMAIN OF HUMAN APLF PROTEIN IN COMPLEX WITH REMARK 900 RIBOFURANOSYLADENOSINE DBREF 2KQC A 368 451 UNP Q8IW19 APLF_HUMAN 368 451 SEQADV 2KQC GLY A 363 UNP Q8IW19 EXPRESSION TAG SEQADV 2KQC PRO A 364 UNP Q8IW19 EXPRESSION TAG SEQADV 2KQC LEU A 365 UNP Q8IW19 EXPRESSION TAG SEQADV 2KQC GLY A 366 UNP Q8IW19 EXPRESSION TAG SEQADV 2KQC SER A 367 UNP Q8IW19 EXPRESSION TAG SEQRES 1 A 89 GLY PRO LEU GLY SER GLY SER GLU GLY ASN LYS VAL LYS SEQRES 2 A 89 ARG THR SER CYS MET TYR GLY ALA ASN CYS TYR ARG LYS SEQRES 3 A 89 ASN PRO VAL HIS PHE GLN HIS PHE SER HIS PRO GLY ASP SEQRES 4 A 89 SER ASP TYR GLY GLY VAL GLN ILE VAL GLY GLN ASP GLU SEQRES 5 A 89 THR ASP ASP ARG PRO GLU CYS PRO TYR GLY PRO SER CYS SEQRES 6 A 89 TYR ARG LYS ASN PRO GLN HIS LYS ILE GLU TYR ARG HIS SEQRES 7 A 89 ASN THR LEU PRO VAL ARG ASN VAL LEU ASP GLU HET ZN A1001 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 2 ASN A 431 TYR A 438 1 8 LINK SG CYS A 421 ZN ZN A1001 1555 1555 2.32 LINK SG CYS A 427 ZN ZN A1001 1555 1555 2.26 LINK NE2 HIS A 434 ZN ZN A1001 1555 1555 1.87 LINK NE2 HIS A 440 ZN ZN A1001 1555 1555 1.88 SITE 1 AC1 4 CYS A 421 CYS A 427 HIS A 434 HIS A 440 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