PDB Short entry for 2KQD HEADER LYASE 04-NOV-09 2KQD TITLE FIRST PBZ DOMAIN OF HUMAN APLF PROTEIN IN COMPLEX WITH TITLE 2 RIBOFURANOSYLADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: APRATAXIN AND PNK-LIKE FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 363-451, PBZ-TYPE 1 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 10 AUTHOR D.NEUHAUS,S.EUSTERMANN,C.BROCKMANN,J.YANG REVDAT 3 29-JUL-20 2KQD 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 16-FEB-10 2KQD 1 JRNL REVDAT 1 19-JAN-10 2KQD 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 2KQD 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_1000101442. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 286; 300 REMARK 210 PH : 6.0; 6.0; 6.0 REMARK 210 IONIC STRENGTH : 0.4; 0.4; 0.4 REMARK 210 PRESSURE : AMBIENT; AMBIENT; 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 0.8 MM [U-98% 13C; U-98% 15N] REMARK 210 APLF_363-451, 2 MM RFA, 95% H2O/ REMARK 210 5% D2O; 20 MM POTASSIUM REMARK 210 PYROPHOSPHATE, 200 MM SODIUM REMARK 210 CHLORIDE, 100 UM ZINC SULPHATE, REMARK 210 2 MM [U-2H] DTT, 0.8 MM [U-98% REMARK 210 13C; U-98% 15N] APLF_363-451, 2 REMARK 210 MM RFA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 FULL-WIDTH; 2D 1H-1H NOESY; 2D REMARK 210 1H-1H NOESY FILTERED; 3D 1H-13C REMARK 210 NOESY; 2D 1H-1H TOCSY 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 : 10 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 363-417 AND CONTAINS F1 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 418-451 ARE NOT SHOWN IN THE COORDINATES BECAUSE STRUCTURE REMARK 400 CALCULATIONS WERE CARRIED OUT ON RESIDUES 363-417 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 O THR A 377 H SER A 397 1.60 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 367 57.31 -142.82 REMARK 500 1 ASN A 372 37.16 -153.72 REMARK 500 1 LYS A 373 40.49 -158.29 REMARK 500 1 TYR A 381 37.37 -140.61 REMARK 500 1 CYS A 385 88.74 -53.02 REMARK 500 1 LYS A 388 111.98 -161.04 REMARK 500 1 GLN A 408 71.87 -105.32 REMARK 500 1 ILE A 409 71.96 50.81 REMARK 500 1 ASP A 413 39.46 -159.27 REMARK 500 2 ASN A 372 -65.90 -145.29 REMARK 500 2 TYR A 381 36.15 -140.54 REMARK 500 2 CYS A 385 92.20 -49.11 REMARK 500 2 ASP A 413 42.67 -144.55 REMARK 500 3 SER A 369 56.48 -117.31 REMARK 500 3 CYS A 385 90.76 -51.92 REMARK 500 3 LYS A 388 84.86 -153.59 REMARK 500 3 VAL A 407 64.89 -115.58 REMARK 500 3 ILE A 409 65.57 -103.71 REMARK 500 3 VAL A 410 77.99 -112.67 REMARK 500 3 THR A 415 66.38 -113.55 REMARK 500 4 ASN A 372 -63.83 -138.53 REMARK 500 4 CYS A 385 87.93 -50.18 REMARK 500 4 PRO A 390 -76.33 -71.59 REMARK 500 4 VAL A 391 -33.16 -38.68 REMARK 500 4 GLN A 408 83.03 -152.60 REMARK 500 4 ILE A 409 76.32 -110.26 REMARK 500 4 VAL A 410 69.35 -115.79 REMARK 500 4 ASP A 413 44.26 -169.15 REMARK 500 5 SER A 369 39.81 -140.20 REMARK 500 5 LYS A 373 75.67 52.63 REMARK 500 5 CYS A 385 85.89 -53.54 REMARK 500 5 VAL A 407 63.95 34.52 REMARK 500 5 ILE A 409 67.24 -111.31 REMARK 500 5 VAL A 410 73.50 -115.18 REMARK 500 6 LEU A 365 -59.79 -142.62 REMARK 500 6 SER A 369 56.44 -142.39 REMARK 500 6 VAL A 410 68.37 -119.39 REMARK 500 6 ASP A 413 40.25 -160.08 REMARK 500 6 GLU A 414 62.26 -114.26 REMARK 500 6 THR A 415 65.21 -113.09 REMARK 500 6 ASP A 416 40.44 -140.57 REMARK 500 7 LEU A 365 78.42 53.14 REMARK 500 7 SER A 367 99.59 54.55 REMARK 500 7 ASN A 372 -58.75 -147.14 REMARK 500 7 CYS A 385 87.50 -49.67 REMARK 500 7 VAL A 407 70.79 -102.83 REMARK 500 7 ILE A 409 69.61 -114.12 REMARK 500 7 VAL A 410 63.93 -118.87 REMARK 500 7 ASP A 413 46.31 -172.25 REMARK 500 7 THR A 415 66.38 -116.35 REMARK 500 REMARK 500 THIS ENTRY HAS 71 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 379 SG REMARK 620 2 CYS A 385 SG 108.4 REMARK 620 3 HIS A 392 NE2 106.6 108.8 REMARK 620 4 HIS A 398 NE2 109.3 112.3 111.2 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR 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: 2KQC RELATED DB: PDB REMARK 900 SECOND PBZ DOMAIN OF HUMAN APLF PROTEIN REMARK 900 RELATED ID: 2KQE RELATED DB: PDB REMARK 900 SECOND PBZ DOMAIN OF HUMAN APLF PROTEIN IN COMPLEX WITH REMARK 900 RIBOFURANOSYLADENOSINE DBREF 2KQD A 368 451 UNP Q8IW19 APLF_HUMAN 368 451 SEQADV 2KQD GLY A 363 UNP Q8IW19 EXPRESSION TAG SEQADV 2KQD PRO A 364 UNP Q8IW19 EXPRESSION TAG SEQADV 2KQD LEU A 365 UNP Q8IW19 EXPRESSION TAG SEQADV 2KQD GLY A 366 UNP Q8IW19 EXPRESSION TAG SEQADV 2KQD 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 HET ADN A1002 31 HET RIB A1003 18 HETNAM ZN ZINC ION HETNAM ADN ADENOSINE HETNAM RIB ALPHA-D-RIBOFURANOSE FORMUL 2 ZN ZN 2+ FORMUL 3 ADN C10 H13 N5 O4 FORMUL 4 RIB C5 H10 O5 HELIX 1 2 VAL A 391 HIS A 395 1 5 LINK O2' ADN A1002 C1 RIB A1003 1555 1555 1.41 LINK SG CYS A 379 ZN ZN A1001 1555 1555 2.26 LINK SG CYS A 385 ZN ZN A1001 1555 1555 2.35 LINK NE2 HIS A 392 ZN ZN A1001 1555 1555 1.93 LINK NE2 HIS A 398 ZN ZN A1001 1555 1555 2.11 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