HEADER DNA BINDING PROTEIN 23-MAR-20 6W9W TITLE R80A PCNA MUTANT DEFECTIVE IN BIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLIFERATING CELL NUCLEAR ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PCNA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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: POL30, YBR088C, YBR0811; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKW336 KEYWDS BIR, BREAK INDUCED REPLICATION, DNA REPAIR, DNA DAMAGE, PCNA, KEYWDS 2 PROLIFERATING CELLULAR NUCLEAR ANTIGEN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.M.RIPLEY,M.T.WASHINGTON REVDAT 2 18-OCT-23 6W9W 1 REMARK REVDAT 1 23-SEP-20 6W9W 0 JRNL AUTH B.M.RIPLEY,M.T.WASHINGTON JRNL TITL STRUCTURAL ANALYSIS OF PCNA MUTANT PROTEINS DEFECTIVE IN JRNL TITL 2 BIR, FF248-249AA AND R80A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 34129 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1676 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 54.5900 - 6.0700 1.00 2713 146 0.1944 0.2062 REMARK 3 2 6.0600 - 4.8200 1.00 2705 130 0.2032 0.1672 REMARK 3 3 4.8100 - 4.2100 1.00 2685 152 0.1645 0.2212 REMARK 3 4 4.2000 - 3.8200 1.00 2682 164 0.2056 0.2436 REMARK 3 5 3.8200 - 3.5500 1.00 2658 192 0.2146 0.2443 REMARK 3 6 3.5500 - 3.3400 1.00 2708 140 0.2220 0.3179 REMARK 3 7 3.3400 - 3.1700 1.00 2747 118 0.2319 0.2594 REMARK 3 8 3.1700 - 3.0300 1.00 2704 122 0.2555 0.3143 REMARK 3 9 3.0300 - 2.9200 1.00 2685 166 0.2721 0.2870 REMARK 3 10 2.9200 - 2.8200 1.00 2710 114 0.2943 0.4401 REMARK 3 11 2.8200 - 2.7300 1.00 2765 103 0.3178 0.3994 REMARK 3 12 2.7300 - 2.6500 1.00 2691 129 0.3418 0.3683 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) : 0.404 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.71 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: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 2042 REMARK 3 ANGLE : 0.606 2756 REMARK 3 CHIRALITY : 0.044 325 REMARK 3 PLANARITY : 0.003 353 REMARK 3 DIHEDRAL : 16.430 764 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6W9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.14 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34129 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 54.595 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.30 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 21.40 REMARK 200 R MERGE FOR SHELL (I) : 0.11300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: POINTLESS REMARK 200 STARTING MODEL: PDB ENTRY 1PLQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULFATE, 0.2 M AMMONIUM REMARK 280 FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 61.03900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.03900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.03900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.03900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 61.03900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.03900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 61.03900 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 61.03900 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 61.03900 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 61.03900 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 61.03900 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 61.03900 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 61.03900 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 61.03900 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 61.03900 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 61.03900 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 61.03900 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 61.03900 REMARK 290 REMARK 290 REMARK: NULL 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: TRIMERIC 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 0.000000 0.000000 1.000000 61.03900 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 183.11700 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 122.07800 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 183.11700 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 122.07800 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 -61.03900 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 PHE A 19 16.62 -145.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 6W9W A 1 254 UNP P15873 PCNA_YEAST 1 254 SEQADV 6W9W HIS A -1 UNP P15873 EXPRESSION TAG SEQADV 6W9W HIS A 0 UNP P15873 EXPRESSION TAG SEQADV 6W9W ALA A 80 UNP P15873 ARG 80 ENGINEERED MUTATION SEQRES 1 A 256 HIS HIS MET LEU GLU ALA LYS PHE GLU GLU ALA SER LEU SEQRES 2 A 256 PHE LYS ARG ILE ILE ASP GLY PHE LYS ASP CYS VAL GLN SEQRES 3 A 256 LEU VAL ASN PHE GLN CYS LYS GLU ASP GLY ILE ILE ALA SEQRES 4 A 256 GLN ALA VAL ASP ASP SER ARG VAL LEU LEU VAL SER LEU SEQRES 5 A 256 GLU ILE GLY VAL GLU ALA PHE GLN GLU TYR ARG CYS ASP SEQRES 6 A 256 HIS PRO VAL THR LEU GLY MET ASP LEU THR SER LEU SER SEQRES 7 A 256 LYS ILE LEU ALA CYS GLY ASN ASN THR ASP THR LEU THR SEQRES 8 A 256 LEU ILE ALA ASP ASN THR PRO ASP SER ILE ILE LEU LEU SEQRES 9 A 256 PHE GLU ASP THR LYS LYS ASP ARG ILE ALA GLU TYR SER SEQRES 10 A 256 LEU LYS LEU MET ASP ILE ASP ALA ASP PHE LEU LYS ILE SEQRES 11 A 256 GLU GLU LEU GLN TYR ASP SER THR LEU SER LEU PRO SER SEQRES 12 A 256 SER GLU PHE SER LYS ILE VAL ARG ASP LEU SER GLN LEU SEQRES 13 A 256 SER ASP SER ILE ASN ILE MET ILE THR LYS GLU THR ILE SEQRES 14 A 256 LYS PHE VAL ALA ASP GLY ASP ILE GLY SER GLY SER VAL SEQRES 15 A 256 ILE ILE LYS PRO PHE VAL ASP MET GLU HIS PRO GLU THR SEQRES 16 A 256 SER ILE LYS LEU GLU MET ASP GLN PRO VAL ASP LEU THR SEQRES 17 A 256 PHE GLY ALA LYS TYR LEU LEU ASP ILE ILE LYS GLY SER SEQRES 18 A 256 SER LEU SER ASP ARG VAL GLY ILE ARG LEU SER SER GLU SEQRES 19 A 256 ALA PRO ALA LEU PHE GLN PHE ASP LEU LYS SER GLY PHE SEQRES 20 A 256 LEU GLN PHE PHE LEU ALA PRO LYS PHE HELIX 1 AA1 ALA A 9 LYS A 20 1 12 HELIX 2 AA2 GLU A 55 PHE A 57 5 3 HELIX 3 AA3 LEU A 72 ALA A 80 1 9 HELIX 4 AA4 SER A 141 GLN A 153 1 13 HELIX 5 AA5 HIS A 190 SER A 194 5 5 HELIX 6 AA6 ALA A 209 ILE A 216 1 8 HELIX 7 AA7 LYS A 217 LEU A 221 5 5 SHEET 1 AA1 5 GLU A 59 CYS A 62 0 SHEET 2 AA1 5 LEU A 2 PHE A 6 -1 N LYS A 5 O GLU A 59 SHEET 3 AA1 5 THR A 87 ALA A 92 -1 O ALA A 92 N LEU A 2 SHEET 4 AA1 5 SER A 98 GLU A 104 -1 O ILE A 100 N ILE A 91 SHEET 5 AA1 5 ILE A 111 LYS A 117 -1 O ALA A 112 N PHE A 103 SHEET 1 AA2 9 VAL A 66 ASP A 71 0 SHEET 2 AA2 9 LEU A 25 LYS A 31 -1 N PHE A 28 O LEU A 68 SHEET 3 AA2 9 GLY A 34 VAL A 40 -1 O GLY A 34 N LYS A 31 SHEET 4 AA2 9 LEU A 46 GLY A 53 -1 O ILE A 52 N ILE A 35 SHEET 5 AA2 9 GLY A 244 LEU A 250 -1 O GLN A 247 N SER A 49 SHEET 6 AA2 9 ALA A 235 LEU A 241 -1 N LEU A 241 O GLY A 244 SHEET 7 AA2 9 ARG A 224 LEU A 229 -1 N GLY A 226 O GLN A 238 SHEET 8 AA2 9 SER A 135 PRO A 140 -1 N LEU A 137 O ILE A 227 SHEET 9 AA2 9 LYS A 196 MET A 199 -1 O GLU A 198 N THR A 136 SHEET 1 AA3 4 SER A 177 ILE A 182 0 SHEET 2 AA3 4 THR A 166 ASP A 172 -1 N PHE A 169 O VAL A 180 SHEET 3 AA3 4 SER A 157 THR A 163 -1 N MET A 161 O LYS A 168 SHEET 4 AA3 4 VAL A 203 GLY A 208 -1 O PHE A 207 N ILE A 158 CISPEP 1 HIS A -1 HIS A 0 0 1.68 CRYST1 122.078 122.078 122.078 90.00 90.00 90.00 P 21 3 12 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 0.008191 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008191 0.00000