HEADER PROTEIN BINDING 11-DEC-12 4ID3 TITLE CRYSTAL STRUCTURE OF THE BRCT DOMAIN OF S. CEREVISIAE REV1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR PROTEIN REV1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BRCT DOMAIN; COMPND 5 SYNONYM: REVERSIONLESS PROTEIN 1; COMPND 6 EC: 2.7.7.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: REV1, YOR346W, O6339; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BRCT DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.M.PRYOR,L.GAKHAR,M.T.WASHINGTON REVDAT 3 24-JAN-18 4ID3 1 AUTHOR REVDAT 2 23-JAN-13 4ID3 1 JRNL REVDAT 1 02-JAN-13 4ID3 0 JRNL AUTH J.M.PRYOR,L.GAKHAR,M.T.WASHINGTON JRNL TITL STRUCTURE AND FUNCTIONAL ANALYSIS OF THE BRCT DOMAIN OF JRNL TITL 2 TRANSLESION SYNTHESIS DNA POLYMERASE REV1. JRNL REF BIOCHEMISTRY V. 52 254 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23240687 JRNL DOI 10.1021/BI301572Z REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1051) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 11404 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 559 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 11.7087 - 3.1076 0.89 2699 139 0.1439 0.2045 REMARK 3 2 3.1076 - 2.4743 0.92 2754 142 0.2311 0.2546 REMARK 3 3 2.4743 - 2.1637 0.93 2787 116 0.2459 0.2521 REMARK 3 4 2.1637 - 1.9669 0.86 2579 140 0.2628 0.3463 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.1300 REMARK 3 OPERATOR: -L,K,H REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1466 REMARK 3 ANGLE : 1.096 1984 REMARK 3 CHIRALITY : 0.069 224 REMARK 3 PLANARITY : 0.004 238 REMARK 3 DIHEDRAL : 11.170 542 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN 'A' AND (RESSEQ 7:93 ) REMARK 3 SELECTION : CHAIN 'B' AND (RESSEQ 7:93 ) REMARK 3 ATOM PAIRS NUMBER : 714 REMARK 3 RMSD : 0.036 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ID3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC BLUE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11413 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 17.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.25500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2EBW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 2000, 0.1M HEPES , PH 7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 41.24550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 159 REMARK 465 SER A 160 REMARK 465 GLN A 161 REMARK 465 SER A 162 REMARK 465 SER A 163 REMARK 465 SER B 159 REMARK 465 SER B 160 REMARK 465 GLN B 161 REMARK 465 SER B 162 REMARK 465 SER B 163 DBREF 4ID3 A 159 250 UNP P12689 REV1_YEAST 159 250 DBREF 4ID3 B 159 250 UNP P12689 REV1_YEAST 159 250 SEQRES 1 A 92 SER SER GLN SER SER LYS ILE PHE LYS ASN CYS VAL ILE SEQRES 2 A 92 TYR ILE ASN GLY TYR THR LYS PRO GLY ARG LEU GLN LEU SEQRES 3 A 92 HIS GLU MET ILE VAL LEU HIS GLY GLY LYS PHE LEU HIS SEQRES 4 A 92 TYR LEU SER SER LYS LYS THR VAL THR HIS ILE VAL ALA SEQRES 5 A 92 SER ASN LEU PRO LEU LYS LYS ARG ILE GLU PHE ALA ASN SEQRES 6 A 92 TYR LYS VAL VAL SER PRO ASP TRP ILE VAL ASP SER VAL SEQRES 7 A 92 LYS GLU ALA ARG LEU LEU PRO TRP GLN ASN TYR SER LEU SEQRES 8 A 92 THR SEQRES 1 B 92 SER SER GLN SER SER LYS ILE PHE LYS ASN CYS VAL ILE SEQRES 2 B 92 TYR ILE ASN GLY TYR THR LYS PRO GLY ARG LEU GLN LEU SEQRES 3 B 92 HIS GLU MET ILE VAL LEU HIS GLY GLY LYS PHE LEU HIS SEQRES 4 B 92 TYR LEU SER SER LYS LYS THR VAL THR HIS ILE VAL ALA SEQRES 5 B 92 SER ASN LEU PRO LEU LYS LYS ARG ILE GLU PHE ALA ASN SEQRES 6 B 92 TYR LYS VAL VAL SER PRO ASP TRP ILE VAL ASP SER VAL SEQRES 7 B 92 LYS GLU ALA ARG LEU LEU PRO TRP GLN ASN TYR SER LEU SEQRES 8 B 92 THR FORMUL 3 HOH *108(H2 O) HELIX 1 1 GLY A 180 HIS A 191 1 12 HELIX 2 2 PRO A 214 PHE A 221 1 8 HELIX 3 3 PRO A 229 ALA A 239 1 11 HELIX 4 4 PRO A 243 SER A 248 5 6 HELIX 5 5 GLY B 180 HIS B 191 1 12 HELIX 6 6 PRO B 214 PHE B 221 1 8 HELIX 7 7 PRO B 229 ALA B 239 1 11 HELIX 8 8 PRO B 243 SER B 248 5 6 SHEET 1 A 4 LYS A 194 LEU A 196 0 SHEET 2 A 4 VAL A 170 ILE A 173 1 N ILE A 171 O LYS A 194 SHEET 3 A 4 HIS A 207 VAL A 209 1 O VAL A 209 N TYR A 172 SHEET 4 A 4 VAL A 226 VAL A 227 1 O VAL A 227 N ILE A 208 SHEET 1 B 4 LYS B 194 LEU B 196 0 SHEET 2 B 4 VAL B 170 ILE B 173 1 N ILE B 171 O LYS B 194 SHEET 3 B 4 HIS B 207 VAL B 209 1 O VAL B 209 N TYR B 172 SHEET 4 B 4 VAL B 226 VAL B 227 1 O VAL B 227 N ILE B 208 CISPEP 1 LYS A 178 PRO A 179 0 -3.74 CISPEP 2 LYS B 178 PRO B 179 0 -3.54 CRYST1 32.003 82.491 32.705 90.00 91.49 90.00 P 1 21 1 4 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 0.031247 0.000000 0.000813 0.00000 SCALE2 0.000000 0.012123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030587 0.00000 MASTER 216 0 0 8 8 0 0 6 0 0 0 16 END