PDB Short entry for 1XPA HEADER DNA REPAIR 06-JUL-98 1XPA TITLE SOLUTION STRUCTURE OF THE DNA-AND RPA-BINDING DOMAIN OF THE HUMAN TITLE 2 REPAIR FACTOR XPA, NMR, 1 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: XPA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MF122, RESIDUES 98-219; COMPND 5 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 BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET16B; SOURCE 9 EXPRESSION_SYSTEM_GENE: HUMAN XPA CDNA KEYWDS DNA REPAIR, NUCLEOTIDE EXCISION REPAIR, ZINC-FINGER EXPDTA SOLUTION NMR AUTHOR T.IKEGAMI,I.KURAOKA,M.SAIJO,N.KODO,Y.KYOGOKU,K.MORIKAWA,K.TANAKA, AUTHOR 2 M.SHIRAKAWA REVDAT 3 02-MAR-22 1XPA 1 REMARK LINK REVDAT 2 24-FEB-09 1XPA 1 VERSN REVDAT 1 22-JUL-99 1XPA 0 JRNL AUTH T.IKEGAMI,I.KURAOKA,M.SAIJO,N.KODO,Y.KYOGOKU,K.MORIKAWA, JRNL AUTH 2 K.TANAKA,M.SHIRAKAWA JRNL TITL SOLUTION STRUCTURE OF THE DNA- AND RPA-BINDING DOMAIN OF THE JRNL TITL 2 HUMAN REPAIR FACTOR XPA. JRNL REF NAT.STRUCT.BIOL. V. 5 701 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9699634 JRNL DOI 10.1038/1400 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177300. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 150MM KCL REMARK 210 PRESSURE : 1 ATMOSPHERE REMARK 210 SAMPLE CONTENTS : 50MM D-TRIS HCL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D-; 4D-MULTI-DIMENSIONAL REMARK 210 EXPERIMENTS REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX500; DRX500; DRX800 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 140 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE LOWEST ENERGY AND NO REMARK 210 VIOLATION GREATER THAN 0.3A OR REMARK 210 5DEG REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED XPA. THIS MODEL IS THE CLOSEST REMARK 210 STRUCTURE TO THE MEAN. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 ARG A 211 REMARK 465 GLU A 212 REMARK 465 LYS A 213 REMARK 465 MET A 214 REMARK 465 LYS A 215 REMARK 465 GLN A 216 REMARK 465 LYS A 217 REMARK 465 LYS A 218 REMARK 465 PHE A 219 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 TYR A 102 33.45 -152.09 REMARK 500 GLU A 107 -50.88 -125.52 REMARK 500 SER A 115 -147.12 -157.32 REMARK 500 ASP A 134 -56.71 -160.23 REMARK 500 LYS A 135 -74.72 -46.33 REMARK 500 LYS A 137 93.46 -48.69 REMARK 500 LEU A 138 163.89 -41.88 REMARK 500 LEU A 149 26.25 43.70 REMARK 500 LYS A 151 -140.44 -123.23 REMARK 500 CYS A 153 -86.25 -127.97 REMARK 500 LEU A 155 -51.30 -125.18 REMARK 500 GLU A 159 85.21 39.13 REMARK 500 LEU A 162 99.96 22.23 REMARK 500 LYS A 163 128.72 -28.73 REMARK 500 ILE A 165 -159.22 -153.15 REMARK 500 LYS A 167 -144.64 -157.72 REMARK 500 HIS A 171 -155.47 -92.58 REMARK 500 ASP A 177 55.81 -158.61 REMARK 500 LEU A 182 105.90 -46.18 REMARK 500 SER A 196 -147.95 179.38 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 ARG A 130 0.28 SIDE CHAIN REMARK 500 ARG A 158 0.27 SIDE CHAIN REMARK 500 ARG A 189 0.32 SIDE CHAIN REMARK 500 ARG A 207 0.31 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 ZN A 220 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 105 SG REMARK 620 2 CYS A 108 SG 106.3 REMARK 620 3 CYS A 126 SG 112.1 109.9 REMARK 620 4 CYS A 129 SG 106.8 112.2 109.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: NUL REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ZN BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 220 DBREF 1XPA A 98 219 UNP P23025 XPA_HUMAN 98 219 SEQRES 1 A 122 MET GLU PHE ASP TYR VAL ILE CYS GLU GLU CYS GLY LYS SEQRES 2 A 122 GLU PHE MET ASP SER TYR LEU MET ASN HIS PHE ASP LEU SEQRES 3 A 122 PRO THR CYS ASP ASN CYS ARG ASP ALA ASP ASP LYS HIS SEQRES 4 A 122 LYS LEU ILE THR LYS THR GLU ALA LYS GLN GLU TYR LEU SEQRES 5 A 122 LEU LYS ASP CYS ASP LEU GLU LYS ARG GLU PRO PRO LEU SEQRES 6 A 122 LYS PHE ILE VAL LYS LYS ASN PRO HIS HIS SER GLN TRP SEQRES 7 A 122 GLY ASP MET LYS LEU TYR LEU LYS LEU GLN ILE VAL LYS SEQRES 8 A 122 ARG SER LEU GLU VAL TRP GLY SER GLN GLU ALA LEU GLU SEQRES 9 A 122 GLU ALA LYS GLU VAL ARG GLN GLU ASN ARG GLU LYS MET SEQRES 10 A 122 LYS GLN LYS LYS PHE HET ZN A 220 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 H1 LYS A 141 GLU A 147 1 7 HELIX 2 H2 LYS A 183 TRP A 194 1 12 HELIX 3 H3 GLN A 197 GLU A 209 1 13 SHEET 1 S1 2 VAL A 103 ILE A 104 0 SHEET 2 S1 2 GLU A 111 PHE A 112 -1 N PHE A 112 O VAL A 103 SHEET 1 S2 3 ILE A 139 THR A 140 0 SHEET 2 S2 3 LEU A 180 TYR A 181 -1 N TYR A 181 O ILE A 139 SHEET 3 S2 3 PHE A 164 ILE A 165 -1 N ILE A 165 O LEU A 180 LINK SG CYS A 105 ZN ZN A 220 1555 1555 2.26 LINK SG CYS A 108 ZN ZN A 220 1555 1555 2.35 LINK SG CYS A 126 ZN ZN A 220 1555 1555 2.44 LINK SG CYS A 129 ZN ZN A 220 1555 1555 2.35 CISPEP 1 GLU A 159 PRO A 160 0 0.07 SITE 1 NUL 4 CYS A 105 CYS A 108 CYS A 126 CYS A 129 SITE 1 AC1 4 CYS A 105 CYS A 108 CYS A 126 CYS A 129 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