HEADER DNA BINDING PROTEIN 27-FEB-99 1XNT TITLE NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN TITLE 2 XRCC1-N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (DNA-REPAIR PROTEIN XRCC1); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152-183 ARE COMPND 5 DISORDERED AND NOT SHOWN.; COMPND 6 SYNONYM: XRCC1-NTD; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELLULAR_LOCATION: NUCLEUS; SOURCE 6 GENE: XRCC1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21[DE3]PLYSS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23A KEYWDS XRCC1, 3D NMR, DNA REPAIR, SINGLE-STRAND BREAK DNA BINDING, DNA KEYWDS 2 POLYMERASE- BETA BINDING, BETA SANDWICH, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 23 AUTHOR A.MARINTCHEV,G.P.MULLEN REVDAT 5 27-DEC-23 1XNT 1 REMARK REVDAT 4 02-MAR-22 1XNT 1 REMARK SEQADV REVDAT 3 24-FEB-09 1XNT 1 VERSN REVDAT 2 01-APR-03 1XNT 1 JRNL REVDAT 1 01-SEP-99 1XNT 0 JRNL AUTH A.MARINTCHEV,M.A.MULLEN,M.W.MACIEJEWSKI,B.PAN,M.R.GRYK, JRNL AUTH 2 G.P.MULLEN JRNL TITL SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN JRNL TITL 2 XRCC1 N-TERMINAL DOMAIN. JRNL REF NAT.STRUCT.BIOL. V. 6 884 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10467102 JRNL DOI 10.1038/12347 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. RMSD (ANGSTROMS) WITH RESPECT TO MEAN: BETA- REMARK 3 STRANDS: HEAVY BACKBONE ATOMS 0.26 +/- 0.05; ALL HEAVY ATOMS REMARK 3 0.69 +/- 0.13. RESIDUES 3-76, 83-151 (EXCLUDING THE FLEXIBLE 77- REMARK 3 82) : HEAVY BACKBONE ATOMS 0.42 +/- 0.09; ALL HEAVY ATOMS 0.87 +/ REMARK 3 - 0.12. REMARK 4 REMARK 4 1XNT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000559. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.4 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : H2O AND D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; CBCA(CO)NH; HN(CO)CA; REMARK 210 15N-EDITED TOCSY; HCC(CO)NH; REMARK 210 HCCH TOCSY; HNCO; HNHA; HNHB; 2D REMARK 210 (HB)CB(CGCD)HD; 1H-15N-HSQC; 1H- REMARK 210 13C-HSQC; 1H-TOCSY; AROMATIC 1H- REMARK 210 13C-HSQC; HMQC-J; 3D 15N-NOESY; REMARK 210 3D 13C-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23 REMARK 210 CONFORMERS, SELECTION CRITERIA : 30 OUT OF 60 STRUCTURES IN REMARK 210 DYANA, CRITERION: TARGET REMARK 210 FUNCTION. X-PLOR REFINEMENT: 23 REMARK 210 OUT OF 30 STRUCTURES, CRITERIA: REMARK 210 NO NOE RESTRAINT VIOLATIONS > REMARK 210 0.5 A AND NO DIHEDRAL ANGLE REMARK 210 RESTRAINT VIOLATIONS > 5 DEG. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE- AND DOUBLE REMARK 210 -RESONANCE NMR SPECTROSCOPY ON 13C-, 15N-LABELED XRCC1-N- REMARK 210 TERMINAL 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 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 MODELS 1-23 REMARK 465 RES C SSSEQI REMARK 465 PRO A 152 REMARK 465 PRO A 153 REMARK 465 ASP A 154 REMARK 465 LYS A 155 REMARK 465 ASP A 156 REMARK 465 GLU A 157 REMARK 465 ALA A 158 REMARK 465 GLU A 159 REMARK 465 ALA A 160 REMARK 465 PRO A 161 REMARK 465 SER A 162 REMARK 465 GLN A 163 REMARK 465 LYS A 164 REMARK 465 VAL A 165 REMARK 465 THR A 166 REMARK 465 VAL A 167 REMARK 465 THR A 168 REMARK 465 LYS A 169 REMARK 465 LEU A 170 REMARK 465 GLY A 171 REMARK 465 GLN A 172 REMARK 465 PHE A 173 REMARK 465 ARG A 174 REMARK 465 VAL A 175 REMARK 465 LYS A 176 REMARK 465 GLU A 177 REMARK 465 GLU A 178 REMARK 465 GLU A 179 REMARK 465 GLU A 180 REMARK 465 SER A 181 REMARK 465 ALA A 182 REMARK 465 ASN A 183 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 SER A 14 73.42 154.40 REMARK 500 1 SER A 17 -63.86 -96.47 REMARK 500 1 LYS A 26 73.61 -119.99 REMARK 500 1 ASP A 28 -116.34 -67.33 REMARK 500 1 THR A 29 -107.78 50.47 REMARK 500 1 TYR A 30 37.42 -179.02 REMARK 500 1 GLU A 40 83.87 -54.39 REMARK 500 1 GLU A 50 -2.60 -56.45 REMARK 500 1 ASP A 63 65.83 -111.71 REMARK 500 1 ALA A 66 -50.17 -135.94 REMARK 500 1 GLN A 82 21.04 -149.55 REMARK 500 1 VAL A 86 88.25 -62.99 REMARK 500 1 VAL A 89 -175.58 -55.46 REMARK 500 1 MET A 94 -157.48 -120.08 REMARK 500 1 SER A 103 89.02 -63.93 REMARK 500 1 ASN A 104 82.03 48.99 REMARK 500 1 GLN A 134 114.88 162.04 REMARK 500 1 LYS A 138 -43.20 -163.18 REMARK 500 1 PHE A 142 -163.53 176.80 REMARK 500 2 SER A 14 74.33 152.73 REMARK 500 2 LYS A 26 62.95 -107.31 REMARK 500 2 THR A 29 -82.74 -156.54 REMARK 500 2 TYR A 30 -38.36 -177.88 REMARK 500 2 GLU A 40 89.85 -48.04 REMARK 500 2 GLU A 50 -9.30 -51.73 REMARK 500 2 ALA A 66 -55.84 -123.37 REMARK 500 2 VAL A 86 86.18 -63.17 REMARK 500 2 VAL A 89 -179.84 -53.13 REMARK 500 2 ARG A 100 -86.43 -73.88 REMARK 500 2 SER A 101 38.80 -161.99 REMARK 500 2 SER A 103 117.24 -175.49 REMARK 500 2 ASN A 104 72.61 40.68 REMARK 500 2 GLN A 134 134.11 157.70 REMARK 500 2 LYS A 138 -41.18 -170.38 REMARK 500 2 PHE A 142 -164.63 -179.74 REMARK 500 3 GLU A 3 -165.55 -79.16 REMARK 500 3 ARG A 7 -51.44 -121.84 REMARK 500 3 SER A 13 59.77 -141.75 REMARK 500 3 SER A 14 59.03 157.22 REMARK 500 3 LYS A 26 68.55 -115.18 REMARK 500 3 THR A 29 -83.06 -156.01 REMARK 500 3 TYR A 30 -37.12 -177.80 REMARK 500 3 GLU A 40 -88.30 -34.11 REMARK 500 3 LYS A 41 -60.07 72.02 REMARK 500 3 GLU A 50 2.59 -59.84 REMARK 500 3 LYS A 51 134.44 -175.97 REMARK 500 3 ALA A 66 -53.45 -141.83 REMARK 500 3 GLN A 82 35.36 -95.78 REMARK 500 3 VAL A 86 85.28 -61.58 REMARK 500 3 VAL A 89 -171.10 -68.73 REMARK 500 REMARK 500 THIS ENTRY HAS 501 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1XNT A 1 183 UNP P18887 XRCC1_HUMAN 1 183 SEQADV 1XNT GLU A 179 UNP P18887 ASP 179 CLONING ARTIFACT SEQRES 1 A 183 MET PRO GLU ILE ARG LEU ARG HIS VAL VAL SER CYS SER SEQRES 2 A 183 SER GLN ASP SER THR HIS CYS ALA GLU ASN LEU LEU LYS SEQRES 3 A 183 ALA ASP THR TYR ARG LYS TRP ARG ALA ALA LYS ALA GLY SEQRES 4 A 183 GLU LYS THR ILE SER VAL VAL LEU GLN LEU GLU LYS GLU SEQRES 5 A 183 GLU GLN ILE HIS SER VAL ASP ILE GLY ASN ASP GLY SER SEQRES 6 A 183 ALA PHE VAL GLU VAL LEU VAL GLY SER SER ALA GLY GLY SEQRES 7 A 183 ALA GLY GLU GLN ASP TYR GLU VAL LEU LEU VAL THR SER SEQRES 8 A 183 SER PHE MET SER PRO SER GLU SER ARG SER GLY SER ASN SEQRES 9 A 183 PRO ASN ARG VAL ARG MET PHE GLY PRO ASP LYS LEU VAL SEQRES 10 A 183 ARG ALA ALA ALA GLU LYS ARG TRP ASP ARG VAL LYS ILE SEQRES 11 A 183 VAL CYS SER GLN PRO TYR SER LYS ASP SER PRO PHE GLY SEQRES 12 A 183 LEU SER PHE VAL ARG PHE HIS SER PRO PRO ASP LYS ASP SEQRES 13 A 183 GLU ALA GLU ALA PRO SER GLN LYS VAL THR VAL THR LYS SEQRES 14 A 183 LEU GLY GLN PHE ARG VAL LYS GLU GLU GLU GLU SER ALA SEQRES 15 A 183 ASN HELIX 1 1 ALA A 21 LEU A 25 5 5 HELIX 2 2 PRO A 96 ARG A 100 1 5 HELIX 3 3 ARG A 118 GLU A 122 1 5 SHEET 1 1 5 HIS A 8 SER A 13 0 SHEET 2 1 5 THR A 42 LEU A 49 -1 N VAL A 46 O SER A 11 SHEET 3 1 5 ARG A 127 SER A 133 -1 N CYS A 132 O ILE A 43 SHEET 4 1 5 PHE A 67 SER A 74 -1 N GLY A 73 O ARG A 127 SHEET 5 1 5 TYR A 84 SER A 92 -1 N LEU A 88 O VAL A 72 SHEET 1 2 3 ARG A 107 GLY A 112 0 SHEET 2 2 3 SER A 57 ASN A 62 -1 N ASN A 62 O ARG A 107 SHEET 3 2 3 PHE A 146 HIS A 150 -1 N HIS A 150 O SER A 57 SHEET 1 3 2 TRP A 33 ALA A 35 0 SHEET 2 3 2 PHE A 142 LEU A 144 -1 N LEU A 144 O TRP A 33 SHEET 1 4 2 GLU A 52 ILE A 55 0 SHEET 2 4 2 ARG A 124 TRP A 125 -1 N TRP A 125 O GLU A 53 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