HEADER LIGASE 27-JAN-04 1UW0 TITLE SOLUTION STRUCTURE OF THE ZINC-FINGER DOMAIN FROM DNA LIGASE IIIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE III; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC-FINGER DOMAIN, RESIDUES 1-117; COMPND 5 SYNONYM: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP]; COMPND 6 EC: 6.5.1.1; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODON PLUS RP; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS DNA REPAIR, ZINC FINGER, LIGASE, PARP-LIKE FINGER, CELL DIVISION, DNA KEYWDS 2 REPLICATION, NUCLEAR PROTEIN EXPDTA SOLUTION NMR NUMMDL 28 AUTHOR A.W.KULCZYK,J.-C.YANG,D.NEUHAUS REVDAT 4 15-MAY-24 1UW0 1 REMARK LINK REVDAT 3 24-FEB-09 1UW0 1 VERSN REVDAT 2 03-MAY-05 1UW0 1 ATOM REVDAT 1 05-AUG-04 1UW0 0 JRNL AUTH A.W.KULCZYK,J.-C.YANG,D.NEUHAUS JRNL TITL SOLUTION STRUCTURE AND DNA BINDING OF THE ZINC-FINGER DOMAIN JRNL TITL 2 FROM DNA LIGASE IIIALPHA JRNL REF J.MOL.BIOL. V. 341 723 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15288782 JRNL DOI 10.1016/J.JMB.2004.06.035 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 1UW0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1290014459. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; HSQC; REMARK 210 CBCANH; CBCACONH; HBHANH; REMARK 210 HBHACONH; HCCH-TOCSY; HCCH-COSY; REMARK 210 15N NOESY-HSQC; 15N HSQC-NOESY- REMARK 210 HSQC; 13C NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, SPARKY, X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 28 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOW RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED DNA-LIGASE III ZINC FINGER REMARK 210 DOMAIN. 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 INTERACTS WITH DNA-REPAIR PROTEIN XRCC1 AND CAN CORRECT REMARK 400 DEFECTIVE DNA STRAND-BREAK REPAIR AND SISTER CHROMATID EXCHANGE REMARK 400 FOLLOWING TREATMENT WITH IONIZING RADIATION AND ALKYLATING REMARK 400 AGENTS. 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 LYS A 22 53.64 -100.74 REMARK 500 1 PHE A 40 -58.34 -149.81 REMARK 500 1 ILE A 70 98.43 54.36 REMARK 500 1 ASP A 72 -165.56 53.34 REMARK 500 1 THR A 74 36.74 -152.96 REMARK 500 1 LEU A 82 173.72 -49.93 REMARK 500 1 SER A 99 -164.90 52.42 REMARK 500 1 LYS A 100 80.06 53.65 REMARK 500 1 ALA A 102 -65.46 -124.91 REMARK 500 1 THR A 104 58.43 -155.42 REMARK 500 1 LYS A 108 81.76 52.40 REMARK 500 2 LYS A 12 -65.68 -138.05 REMARK 500 2 CYS A 21 148.70 -172.49 REMARK 500 2 LYS A 22 45.99 -107.45 REMARK 500 2 PHE A 40 100.11 55.26 REMARK 500 2 ILE A 70 101.83 55.18 REMARK 500 2 ASP A 72 -173.06 53.17 REMARK 500 2 THR A 74 50.23 -102.80 REMARK 500 2 LEU A 82 -179.87 -53.25 REMARK 500 2 SER A 98 46.73 -100.67 REMARK 500 2 LYS A 100 48.98 -144.89 REMARK 500 2 ALA A 101 56.97 -141.67 REMARK 500 2 ALA A 102 57.65 -145.08 REMARK 500 2 LYS A 107 179.91 53.19 REMARK 500 3 LYS A 22 44.66 -105.38 REMARK 500 3 VAL A 26 112.95 -165.45 REMARK 500 3 LYS A 27 126.76 60.47 REMARK 500 3 PHE A 40 -58.74 -147.33 REMARK 500 3 ILE A 70 98.29 54.41 REMARK 500 3 ASP A 72 -166.01 53.33 REMARK 500 3 THR A 74 38.04 -149.28 REMARK 500 3 LEU A 82 -175.06 -69.81 REMARK 500 3 SER A 98 -65.50 -96.44 REMARK 500 3 SER A 99 94.70 52.39 REMARK 500 4 GLN A 4 107.92 57.68 REMARK 500 4 LYS A 22 51.27 -101.09 REMARK 500 4 LYS A 27 142.40 59.91 REMARK 500 4 PHE A 40 -58.83 -148.00 REMARK 500 4 ILE A 70 97.97 53.78 REMARK 500 4 ASP A 72 -170.54 53.08 REMARK 500 4 LEU A 82 -165.85 -113.28 REMARK 500 4 LYS A 100 -59.70 -143.44 REMARK 500 4 THR A 104 73.49 52.57 REMARK 500 4 LYS A 106 -60.18 -131.78 REMARK 500 5 CYS A 21 -44.45 -172.98 REMARK 500 5 LYS A 22 44.15 70.08 REMARK 500 5 LYS A 27 102.82 53.94 REMARK 500 5 PHE A 40 -58.37 -152.90 REMARK 500 5 ILE A 70 94.71 52.84 REMARK 500 5 ASP A 72 -165.25 53.46 REMARK 500 REMARK 500 THIS ENTRY HAS 256 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 1 ARG A 5 0.31 SIDE CHAIN REMARK 500 1 ARG A 13 0.26 SIDE CHAIN REMARK 500 1 ARG A 31 0.20 SIDE CHAIN REMARK 500 1 ARG A 62 0.23 SIDE CHAIN REMARK 500 1 ARG A 64 0.25 SIDE CHAIN REMARK 500 2 ARG A 5 0.28 SIDE CHAIN REMARK 500 2 ARG A 13 0.22 SIDE CHAIN REMARK 500 2 ARG A 31 0.20 SIDE CHAIN REMARK 500 2 ARG A 62 0.22 SIDE CHAIN REMARK 500 2 ARG A 64 0.24 SIDE CHAIN REMARK 500 3 ARG A 5 0.29 SIDE CHAIN REMARK 500 3 ARG A 13 0.32 SIDE CHAIN REMARK 500 3 ARG A 31 0.32 SIDE CHAIN REMARK 500 3 ARG A 62 0.25 SIDE CHAIN REMARK 500 3 ARG A 64 0.31 SIDE CHAIN REMARK 500 4 ARG A 5 0.24 SIDE CHAIN REMARK 500 4 ARG A 13 0.23 SIDE CHAIN REMARK 500 4 ARG A 31 0.24 SIDE CHAIN REMARK 500 4 ARG A 62 0.27 SIDE CHAIN REMARK 500 4 ARG A 64 0.22 SIDE CHAIN REMARK 500 5 ARG A 5 0.31 SIDE CHAIN REMARK 500 5 ARG A 13 0.27 SIDE CHAIN REMARK 500 5 ARG A 31 0.23 SIDE CHAIN REMARK 500 5 ARG A 62 0.27 SIDE CHAIN REMARK 500 5 ARG A 64 0.32 SIDE CHAIN REMARK 500 6 ARG A 5 0.26 SIDE CHAIN REMARK 500 6 ARG A 13 0.31 SIDE CHAIN REMARK 500 6 ARG A 31 0.23 SIDE CHAIN REMARK 500 6 ARG A 62 0.31 SIDE CHAIN REMARK 500 6 ARG A 64 0.26 SIDE CHAIN REMARK 500 7 ARG A 5 0.22 SIDE CHAIN REMARK 500 7 ARG A 13 0.22 SIDE CHAIN REMARK 500 7 ARG A 31 0.29 SIDE CHAIN REMARK 500 7 ARG A 62 0.25 SIDE CHAIN REMARK 500 7 ARG A 64 0.28 SIDE CHAIN REMARK 500 8 ARG A 5 0.32 SIDE CHAIN REMARK 500 8 ARG A 13 0.30 SIDE CHAIN REMARK 500 8 ARG A 31 0.22 SIDE CHAIN REMARK 500 8 ARG A 62 0.24 SIDE CHAIN REMARK 500 8 ARG A 64 0.31 SIDE CHAIN REMARK 500 9 ARG A 5 0.32 SIDE CHAIN REMARK 500 9 ARG A 13 0.23 SIDE CHAIN REMARK 500 9 ARG A 31 0.29 SIDE CHAIN REMARK 500 9 ARG A 62 0.23 SIDE CHAIN REMARK 500 9 ARG A 64 0.29 SIDE CHAIN REMARK 500 10 ARG A 5 0.23 SIDE CHAIN REMARK 500 10 ARG A 13 0.31 SIDE CHAIN REMARK 500 10 ARG A 31 0.26 SIDE CHAIN REMARK 500 10 ARG A 62 0.28 SIDE CHAIN REMARK 500 10 ARG A 64 0.32 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 140 PLANE DEVIATIONS. 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 A1118 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 CYS A 21 SG 101.6 REMARK 620 3 HIS A 52 ND1 97.9 117.9 REMARK 620 4 CYS A 55 SG 117.1 102.6 119.1 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 A1118 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IMO RELATED DB: PDB REMARK 900 NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN REMARK 900 RELATED ID: 1IN1 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN DBREF 1UW0 A 1 117 UNP P49916 DNL3_HUMAN 1 117 SEQRES 1 A 117 MET ALA GLU GLN ARG PHE CYS VAL ASP TYR ALA LYS ARG SEQRES 2 A 117 GLY THR ALA GLY CYS LYS LYS CYS LYS GLU LYS ILE VAL SEQRES 3 A 117 LYS GLY VAL CYS ARG ILE GLY LYS VAL VAL PRO ASN PRO SEQRES 4 A 117 PHE SER GLU SER GLY GLY ASP MET LYS GLU TRP TYR HIS SEQRES 5 A 117 ILE LYS CYS MET PHE GLU LYS LEU GLU ARG ALA ARG ALA SEQRES 6 A 117 THR THR LYS LYS ILE GLU ASP LEU THR GLU LEU GLU GLY SEQRES 7 A 117 TRP GLU GLU LEU GLU ASP ASN GLU LYS GLU GLN ILE THR SEQRES 8 A 117 GLN HIS ILE ALA ASP LEU SER SER LYS ALA ALA GLY THR SEQRES 9 A 117 PRO LYS LYS LYS ALA VAL VAL GLN ALA LYS LEU THR THR HET ZN A1118 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 HIS A 52 ALA A 63 1 12 HELIX 2 2 GLU A 83 SER A 99 1 17 SHEET 1 AA 3 ARG A 5 TYR A 10 0 SHEET 2 AA 3 CYS A 30 PRO A 37 -1 O ARG A 31 N ASP A 9 SHEET 3 AA 3 ASP A 46 MET A 47 -1 O MET A 47 N VAL A 36 SHEET 1 AB 2 ALA A 16 GLY A 17 0 SHEET 2 AB 2 LYS A 24 ILE A 25 -1 O ILE A 25 N ALA A 16 LINK SG CYS A 18 ZN ZN A1118 1555 1555 2.29 LINK SG CYS A 21 ZN ZN A1118 1555 1555 2.30 LINK ND1 HIS A 52 ZN ZN A1118 1555 1555 2.03 LINK SG CYS A 55 ZN ZN A1118 1555 1555 2.32 SITE 1 AC1 4 CYS A 18 CYS A 21 HIS A 52 CYS A 55 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