HEADER DNA BINDING PROTEIN 26-JAN-05 1YNX TITLE SOLUTION STRUCTURE OF DNA BINDING DOMAIN A (DBD-A) OF S.CEREVISIAE TITLE 2 REPLICATION PROTEIN A (RPA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION FACTOR-A PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA BINDING DOMAIN A; COMPND 5 SYNONYM: REPLICATION PROTEIN A, RF-A, SINGLE-STRANDED DNA-BINDING COMPND 6 PROTEIN, DNA BINDING PROTEIN BUF2, REPLICATION PROTEIN A 69 KDA DNA- COMPND 7 BINDING SUBUNIT; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: RFA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS CANONICAL OB FOLD, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 22 AUTHOR C.J.PARK,J.H.LEE,B.S.CHOI REVDAT 3 02-MAR-22 1YNX 1 REMARK REVDAT 2 24-FEB-09 1YNX 1 VERSN REVDAT 1 10-JAN-06 1YNX 0 JRNL AUTH C.J.PARK,J.H.LEE,B.S.CHOI JRNL TITL SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF RPA FROM JRNL TITL 2 SACCHAROMYCES CEREVISIAE AND ITS INTERACTION WITH JRNL TITL 3 SINGLE-STRANDED DNA AND SV40 T ANTIGEN JRNL REF NUCLEIC ACIDS RES. V. 33 4172 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 16043636 JRNL DOI 10.1093/NAR/GKI736 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE LATEST, X-PLOR NIH 2.9.6 REMARK 3 AUTHORS : DELAGLIO ET AL. (NMRPIPE), CLORE ET AL., (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE CALCULATIONS WERE REMARK 3 PERFORMED USING 1138 INTERPROTON DISTANCE RESTRAINTS AND 161 REMARK 3 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1YNX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031733. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM SCRPA DBD A U-15N, 13C; 20MM REMARK 210 SODIUM PHOSPHATE, 100MM NACL, REMARK 210 2MM DTT, PH 7.0; 90% H2O, 10% REMARK 210 D2O; 1MM SCRPA DBD A U-15N; 20MM REMARK 210 SODIUM PHOSPHATE, 100MM NACL, REMARK 210 2MM DTT, PH 7.0; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_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 : VNMR LATEST, X-PLOR NIH 2.9.6 REMARK 210 METHOD USED : TORSIONAL ANGLE DYNAMICS WITH REMARK 210 INTERNAL VARIABLE MODULE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 22 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 12 REMARK 210 REMARK 210 REMARK: THE CHEMICAL SHIFT ASSIGNMENTS WERE DONE WITH TRIPLE REMARK 210 -RESONANCE EXPERIMENTS. RESTRAINTS WERE GET FROM 3D 13C, 15N REMARK 210 NOESY DATA. 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: 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 VAL A 196 89.20 -176.21 REMARK 500 1 GLU A 208 -165.73 -174.62 REMARK 500 1 PHE A 238 -156.13 -86.62 REMARK 500 1 ASN A 239 -140.49 -52.22 REMARK 500 1 ASP A 240 -32.78 -34.58 REMARK 500 1 GLN A 250 -161.98 -111.57 REMARK 500 1 LYS A 259 61.55 61.67 REMARK 500 1 ASP A 281 -50.17 -164.15 REMARK 500 1 ARG A 282 -151.84 -75.81 REMARK 500 2 LEU A 190 156.81 -47.82 REMARK 500 2 GLN A 194 90.98 -61.85 REMARK 500 2 SER A 204 -50.63 -122.72 REMARK 500 2 GLU A 208 174.16 50.46 REMARK 500 2 ASN A 214 -155.52 -162.19 REMARK 500 2 ASN A 239 -141.04 -36.43 REMARK 500 2 ASP A 240 -33.69 -35.84 REMARK 500 2 GLN A 250 -162.30 -111.34 REMARK 500 2 LYS A 259 120.93 56.58 REMARK 500 2 ALA A 260 164.82 175.78 REMARK 500 2 ASP A 281 -54.04 -163.22 REMARK 500 2 ARG A 282 -150.30 -69.48 REMARK 500 3 GLU A 208 169.99 53.88 REMARK 500 3 ASN A 239 -141.10 -44.43 REMARK 500 3 ASP A 240 -30.75 -37.52 REMARK 500 3 GLN A 250 -161.93 -113.75 REMARK 500 3 LYS A 259 120.32 57.05 REMARK 500 3 ALA A 260 161.01 176.09 REMARK 500 3 ASP A 281 -85.31 -121.88 REMARK 500 3 PHE A 290 -65.82 -163.68 REMARK 500 4 GLN A 194 97.77 -53.43 REMARK 500 4 SER A 204 -51.50 -121.23 REMARK 500 4 GLU A 208 175.86 50.63 REMARK 500 4 HIS A 213 -168.57 53.49 REMARK 500 4 ASN A 214 -82.41 179.34 REMARK 500 4 ASN A 239 -140.16 -51.28 REMARK 500 4 ASP A 240 -33.70 -34.09 REMARK 500 4 GLN A 250 -162.21 -114.83 REMARK 500 4 LYS A 259 112.21 55.26 REMARK 500 4 ALA A 260 167.47 174.02 REMARK 500 4 ASP A 281 -82.66 -123.92 REMARK 500 4 ARG A 282 -52.76 -128.83 REMARK 500 5 PRO A 183 -169.75 -68.36 REMARK 500 5 ALA A 201 179.13 178.43 REMARK 500 5 GLU A 208 -150.46 -173.34 REMARK 500 5 HIS A 213 62.92 -103.41 REMARK 500 5 PHE A 238 -166.83 -62.79 REMARK 500 5 ASN A 239 -141.93 -55.66 REMARK 500 5 ASP A 240 -33.18 -37.32 REMARK 500 5 GLN A 250 -162.01 -106.65 REMARK 500 5 LYS A 259 62.07 64.65 REMARK 500 REMARK 500 THIS ENTRY HAS 230 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 182 0.24 SIDE CHAIN REMARK 500 1 ARG A 202 0.31 SIDE CHAIN REMARK 500 1 ARG A 216 0.23 SIDE CHAIN REMARK 500 1 ARG A 234 0.24 SIDE CHAIN REMARK 500 1 ARG A 282 0.18 SIDE CHAIN REMARK 500 2 ARG A 182 0.26 SIDE CHAIN REMARK 500 2 ARG A 202 0.19 SIDE CHAIN REMARK 500 2 ARG A 216 0.32 SIDE CHAIN REMARK 500 2 ARG A 234 0.27 SIDE CHAIN REMARK 500 2 ARG A 282 0.32 SIDE CHAIN REMARK 500 3 ARG A 182 0.22 SIDE CHAIN REMARK 500 3 ARG A 202 0.32 SIDE CHAIN REMARK 500 3 ARG A 216 0.31 SIDE CHAIN REMARK 500 3 ARG A 234 0.32 SIDE CHAIN REMARK 500 3 ARG A 282 0.32 SIDE CHAIN REMARK 500 4 ARG A 182 0.25 SIDE CHAIN REMARK 500 4 ARG A 202 0.30 SIDE CHAIN REMARK 500 4 ARG A 216 0.31 SIDE CHAIN REMARK 500 4 ARG A 234 0.31 SIDE CHAIN REMARK 500 4 ARG A 282 0.32 SIDE CHAIN REMARK 500 5 ARG A 182 0.21 SIDE CHAIN REMARK 500 5 ARG A 202 0.18 SIDE CHAIN REMARK 500 5 ARG A 216 0.31 SIDE CHAIN REMARK 500 5 ARG A 234 0.27 SIDE CHAIN REMARK 500 5 ARG A 282 0.23 SIDE CHAIN REMARK 500 6 ARG A 182 0.17 SIDE CHAIN REMARK 500 6 ARG A 202 0.26 SIDE CHAIN REMARK 500 6 ARG A 216 0.30 SIDE CHAIN REMARK 500 6 ARG A 234 0.25 SIDE CHAIN REMARK 500 6 ARG A 282 0.27 SIDE CHAIN REMARK 500 7 ARG A 182 0.26 SIDE CHAIN REMARK 500 7 ARG A 202 0.21 SIDE CHAIN REMARK 500 7 ARG A 216 0.27 SIDE CHAIN REMARK 500 7 ARG A 234 0.28 SIDE CHAIN REMARK 500 7 ARG A 282 0.31 SIDE CHAIN REMARK 500 8 ARG A 182 0.28 SIDE CHAIN REMARK 500 8 ARG A 202 0.23 SIDE CHAIN REMARK 500 8 ARG A 216 0.31 SIDE CHAIN REMARK 500 8 ARG A 234 0.27 SIDE CHAIN REMARK 500 8 ARG A 282 0.29 SIDE CHAIN REMARK 500 9 ARG A 182 0.23 SIDE CHAIN REMARK 500 9 ARG A 202 0.32 SIDE CHAIN REMARK 500 9 ARG A 216 0.26 SIDE CHAIN REMARK 500 9 ARG A 234 0.26 SIDE CHAIN REMARK 500 9 ARG A 282 0.23 SIDE CHAIN REMARK 500 10 ARG A 182 0.32 SIDE CHAIN REMARK 500 10 ARG A 202 0.26 SIDE CHAIN REMARK 500 10 ARG A 216 0.25 SIDE CHAIN REMARK 500 10 ARG A 234 0.23 SIDE CHAIN REMARK 500 10 ARG A 282 0.17 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 110 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FGU RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE HUMAN HOMOLOG WITHOUT DNA REMARK 900 RELATED ID: 1JMC RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN HOMOLOG WITH DNA DBREF 1YNX A 181 294 UNP P22336 RFA1_YEAST 181 294 SEQRES 1 A 114 THR ARG PRO ILE PHE ALA ILE GLU GLN LEU SER PRO TYR SEQRES 2 A 114 GLN ASN VAL TRP THR ILE LYS ALA ARG VAL SER TYR LYS SEQRES 3 A 114 GLY GLU ILE LYS THR TRP HIS ASN GLN ARG GLY ASP GLY SEQRES 4 A 114 LYS LEU PHE ASN VAL ASN PHE LEU ASP THR SER GLY GLU SEQRES 5 A 114 ILE ARG ALA THR ALA PHE ASN ASP PHE ALA THR LYS PHE SEQRES 6 A 114 ASN GLU ILE LEU GLN GLU GLY LYS VAL TYR TYR VAL SER SEQRES 7 A 114 LYS ALA LYS LEU GLN PRO ALA LYS PRO GLN PHE THR ASN SEQRES 8 A 114 LEU THR HIS PRO TYR GLU LEU ASN LEU ASP ARG ASP THR SEQRES 9 A 114 VAL ILE GLU GLU CYS PHE ASP GLU SER ASN HELIX 1 1 ALA A 186 LEU A 190 5 5 HELIX 2 2 PHE A 238 LEU A 249 1 12 SHEET 1 A 7 LYS A 261 PRO A 264 0 SHEET 2 A 7 TYR A 276 LEU A 280 -1 O GLU A 277 N GLN A 263 SHEET 3 A 7 GLY A 231 ALA A 237 1 N THR A 236 O LEU A 280 SHEET 4 A 7 ASP A 218 ASP A 228 -1 N VAL A 224 O ALA A 235 SHEET 5 A 7 THR A 198 HIS A 213 -1 N LYS A 210 O LEU A 221 SHEET 6 A 7 VAL A 254 SER A 258 -1 O VAL A 257 N ILE A 199 SHEET 7 A 7 VAL A 285 GLU A 288 -1 O VAL A 285 N SER A 258 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