PDB Short entry for 1D4U HEADER DNA BINDING PROTEIN 06-OCT-99 1D4U TITLE INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH TITLE 2 RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION STUDIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOTIDE EXCISION REPAIR PROTEIN XPA (XPA-MBD); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: XPA-MBD; 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11D KEYWDS DNA REPAIR, LOOP-RICH DOMAIN, NMR RELAXATION, DNA BINDING PROTEIN EXPDTA SOLUTION NMR AUTHOR G.W.BUCHKO,G.W.DAUGHDRILL,R.DE LORIMIER,S.RAO,N.G.ISERN,J.LINGBECK, AUTHOR 2 J.TAYLOR,M.S.WOLD,M.GOCHIN,L.D.SPICER,D.F.LOWRY,M.A.KENNEDY REVDAT 5 16-FEB-22 1D4U 1 REMARK LINK REVDAT 4 24-FEB-09 1D4U 1 VERSN REVDAT 3 01-APR-03 1D4U 1 JRNL REVDAT 2 12-JAN-00 1D4U 1 JRNL REVDAT 1 17-OCT-99 1D4U 0 JRNL AUTH G.W.BUCHKO,G.W.DAUGHDRILL,R.DE LORIMIER,K.RAO B,N.G.ISERN, JRNL AUTH 2 J.M.LINGBECK,J.S.TAYLOR,M.S.WOLD,M.GOCHIN,L.D.SPICER, JRNL AUTH 3 D.F.LOWRY,M.A.KENNEDY JRNL TITL INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA JRNL TITL 2 WITH DNA AND RPA70 DELTA C327: CHEMICAL SHIFT MAPPING AND JRNL TITL 3 15N NMR RELAXATION STUDIES. JRNL REF BIOCHEMISTRY V. 38 15116 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10563794 JRNL DOI 10.1021/BI991755P REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER, A.T. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PARAMAGNETIC PSEUDOCONTACT SHIFTS WERE REMARK 3 USED IN THE REFINEMENT. REMARK 4 REMARK 4 1D4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009794. 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 REMARK 210 PRESSURE : 1ATM. REMARK 210 SAMPLE CONTENTS : 50MM TRIS-HCL;PH7.3,150MM KCL, REMARK 210 25MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HNCACB; REMARK 210 HCCH-TOCSY; HCCH-TOCSY-NNH; HNCO; REMARK 210 CBCA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: 3D NOESY AND TOCSY SPECTRA WERE COLLECTED ON THE CO2+ REMARK 210 SUBSTITUTED XPA-MBD. 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 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 GLU A 2 121.03 68.83 REMARK 500 ASP A 4 38.00 177.26 REMARK 500 GLU A 14 157.17 -44.53 REMARK 500 PHE A 15 -161.60 169.72 REMARK 500 MET A 16 -35.58 -158.00 REMARK 500 ASP A 17 134.15 -170.43 REMARK 500 SER A 18 -105.36 -139.90 REMARK 500 HIS A 23 42.52 -146.64 REMARK 500 PHE A 24 -33.06 -146.97 REMARK 500 ASP A 25 25.54 96.48 REMARK 500 PRO A 27 -83.50 -66.78 REMARK 500 THR A 28 -176.53 49.20 REMARK 500 ASP A 30 44.57 -83.86 REMARK 500 ASP A 31 -44.53 -132.63 REMARK 500 ARG A 33 -169.58 47.13 REMARK 500 ASP A 34 -33.38 -170.12 REMARK 500 ASP A 36 -16.54 75.54 REMARK 500 ASP A 37 -4.14 -142.97 REMARK 500 LYS A 38 -23.47 -173.70 REMARK 500 LYS A 40 119.97 -35.85 REMARK 500 LEU A 41 -176.09 -58.72 REMARK 500 LEU A 52 45.73 70.46 REMARK 500 LYS A 54 82.36 -164.95 REMARK 500 ASP A 55 169.32 76.71 REMARK 500 CYS A 56 -13.67 81.83 REMARK 500 GLU A 62 64.09 75.40 REMARK 500 PRO A 64 41.97 -80.40 REMARK 500 VAL A 69 101.94 -171.58 REMARK 500 LYS A 70 -177.24 172.60 REMARK 500 HIS A 75 172.55 -54.79 REMARK 500 SER A 76 115.01 58.61 REMARK 500 VAL A 96 -74.11 -86.68 REMARK 500 SER A 99 148.15 -174.23 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 33 0.32 SIDE CHAIN REMARK 500 ARG A 61 0.18 SIDE CHAIN REMARK 500 ARG A 92 0.28 SIDE CHAIN REMARK 500 ARG A 110 0.26 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 112 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 CYS A 11 SG 111.3 REMARK 620 3 CYS A 29 SG 114.1 111.7 REMARK 620 4 CYS A 32 SG 110.2 98.3 110.1 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 112 DBREF 1D4U A 1 111 UNP P23025 XPA_HUMAN 40 150 SEQRES 1 A 111 MET GLU PHE ASP TYR VAL ILE CYS GLU GLU CYS GLY LYS SEQRES 2 A 111 GLU PHE MET ASP SER TYR LEU MET ASP HIS PHE ASP LEU SEQRES 3 A 111 PRO THR CYS ASP ASP CYS ARG ASP ALA ASP ASP LYS HIS SEQRES 4 A 111 LYS LEU ILE THR LYS THR GLU ALA LYS GLN GLU TYR LEU SEQRES 5 A 111 LEU LYS ASP CYS ASP LEU GLU LYS ARG GLU PRO PRO LEU SEQRES 6 A 111 LYS PHE ILE VAL LYS LYS ASN PRO HIS HIS SER GLN TRP SEQRES 7 A 111 GLY ASP MET LYS LEU TYR LEU LYS LEU GLN ILE VAL LYS SEQRES 8 A 111 ARG SER LEU GLU VAL TRP GLY SER GLN GLU ALA LEU GLU SEQRES 9 A 111 GLU ALA LYS GLU VAL ARG GLN HET ZN A 112 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 LYS A 44 LYS A 48 1 5 HELIX 2 2 LEU A 85 TRP A 97 1 13 HELIX 3 3 SER A 99 ARG A 110 1 12 SHEET 1 A 2 VAL A 6 ILE A 7 0 SHEET 2 A 2 GLU A 14 PHE A 15 -1 O PHE A 15 N VAL A 6 SHEET 1 B 3 ILE A 42 THR A 43 0 SHEET 2 B 3 LYS A 82 TYR A 84 -1 O TYR A 84 N ILE A 42 SHEET 3 B 3 PHE A 67 VAL A 69 -1 O ILE A 68 N LEU A 83 LINK SG CYS A 8 ZN ZN A 112 1555 1555 2.29 LINK SG CYS A 11 ZN ZN A 112 1555 1555 2.36 LINK SG CYS A 29 ZN ZN A 112 1555 1555 2.30 LINK SG CYS A 32 ZN ZN A 112 1555 1555 2.40 SITE 1 AC1 4 CYS A 8 CYS A 11 CYS A 29 CYS A 32 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