HEADER DNA BINDING PROTEIN 25-MAR-20 6WAC TITLE FF248-249AA 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 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 6WAC 1 REMARK REVDAT 1 30-SEP-20 6WAC 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. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 12383 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 594 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 60.2800 - 4.6000 0.98 2937 151 0.2024 0.2201 REMARK 3 2 4.6000 - 3.6500 0.98 2983 125 0.2352 0.2630 REMARK 3 3 3.6500 - 3.1900 0.99 2924 186 0.2773 0.3403 REMARK 3 4 3.1900 - 2.9000 0.98 2945 132 0.3654 0.4124 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) : 0.500 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 82.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.02 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 1999 REMARK 3 ANGLE : 0.532 2697 REMARK 3 CHIRALITY : 0.043 322 REMARK 3 PLANARITY : 0.004 345 REMARK 3 DIHEDRAL : 16.915 755 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 6WAC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247878. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 1.000 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 : TRUNCATE REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12383 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 60.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.83700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 1PLQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE HEXAHYDRATE, SODIUM REMARK 280 DIMETHYLARSINIC ACID, PEG1000, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.44050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.08038 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.57467 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 43.44050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 25.08038 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.57467 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 43.44050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 25.08038 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.57467 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.16077 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 67.14933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 50.16077 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 67.14933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 50.16077 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 67.14933 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OG SER A 222 O ASP A 240 2.17 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 CYS A 22 -75.44 -65.84 REMARK 500 LEU A 25 71.92 57.85 REMARK 500 VAL A 45 -31.00 -130.97 REMARK 500 GLU A 59 110.52 -164.65 REMARK 500 PRO A 65 97.23 -69.76 REMARK 500 ASP A 204 86.06 -151.24 REMARK 500 LYS A 242 97.24 -69.41 REMARK 500 PRO A 252 -162.65 -72.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 6WAC A 1 253 UNP P15873 PCNA_YEAST 1 253 SEQADV 6WAC ALA A 248 UNP P15873 PHE 248 ENGINEERED MUTATION SEQADV 6WAC ALA A 249 UNP P15873 PHE 249 ENGINEERED MUTATION SEQRES 1 A 253 MET LEU GLU ALA LYS PHE GLU GLU ALA SER LEU PHE LYS SEQRES 2 A 253 ARG ILE ILE ASP GLY PHE LYS ASP CYS VAL GLN LEU VAL SEQRES 3 A 253 ASN PHE GLN CYS LYS GLU ASP GLY ILE ILE ALA GLN ALA SEQRES 4 A 253 VAL ASP ASP SER ARG VAL LEU LEU VAL SER LEU GLU ILE SEQRES 5 A 253 GLY VAL GLU ALA PHE GLN GLU TYR ARG CYS ASP HIS PRO SEQRES 6 A 253 VAL THR LEU GLY MET ASP LEU THR SER LEU SER LYS ILE SEQRES 7 A 253 LEU ARG CYS GLY ASN ASN THR ASP THR LEU THR LEU ILE SEQRES 8 A 253 ALA ASP ASN THR PRO ASP SER ILE ILE LEU LEU PHE GLU SEQRES 9 A 253 ASP THR LYS LYS ASP ARG ILE ALA GLU TYR SER LEU LYS SEQRES 10 A 253 LEU MET ASP ILE ASP ALA ASP PHE LEU LYS ILE GLU GLU SEQRES 11 A 253 LEU GLN TYR ASP SER THR LEU SER LEU PRO SER SER GLU SEQRES 12 A 253 PHE SER LYS ILE VAL ARG ASP LEU SER GLN LEU SER ASP SEQRES 13 A 253 SER ILE ASN ILE MET ILE THR LYS GLU THR ILE LYS PHE SEQRES 14 A 253 VAL ALA ASP GLY ASP ILE GLY SER GLY SER VAL ILE ILE SEQRES 15 A 253 LYS PRO PHE VAL ASP MET GLU HIS PRO GLU THR SER ILE SEQRES 16 A 253 LYS LEU GLU MET ASP GLN PRO VAL ASP LEU THR PHE GLY SEQRES 17 A 253 ALA LYS TYR LEU LEU ASP ILE ILE LYS GLY SER SER LEU SEQRES 18 A 253 SER ASP ARG VAL GLY ILE ARG LEU SER SER GLU ALA PRO SEQRES 19 A 253 ALA LEU PHE GLN PHE ASP LEU LYS SER GLY PHE LEU GLN SEQRES 20 A 253 ALA ALA LEU ALA PRO LYS HELIX 1 AA1 GLU A 8 PHE A 19 1 12 HELIX 2 AA2 ASP A 71 ARG A 80 1 10 HELIX 3 AA3 SER A 141 SER A 152 1 12 HELIX 4 AA4 ALA A 209 ILE A 216 1 8 HELIX 5 AA5 LYS A 217 LEU A 221 5 5 SHEET 1 AA1 5 PHE A 57 CYS A 62 0 SHEET 2 AA1 5 LEU A 2 PHE A 6 -1 N GLU A 3 O ARG A 61 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 GLU A 104 N THR A 87 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 MET A 70 0 SHEET 2 AA2 9 VAL A 26 CYS A 30 -1 N CYS A 30 O VAL A 66 SHEET 3 AA2 9 GLY A 34 VAL A 40 -1 O ILE A 36 N GLN A 29 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 PHE A 239 O LEU A 246 SHEET 7 AA2 9 ARG A 224 LEU A 229 -1 N ARG A 228 O LEU A 236 SHEET 8 AA2 9 SER A 135 PRO A 140 -1 N SER A 135 O LEU A 229 SHEET 9 AA2 9 LYS A 196 MET A 199 -1 O LYS A 196 N SER A 138 SHEET 1 AA3 4 SER A 177 ILE A 182 0 SHEET 2 AA3 4 THR A 166 ASP A 172 -1 N ILE A 167 O ILE A 182 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 LEU A 205 N ILE A 160 CRYST1 86.881 86.881 100.724 90.00 90.00 120.00 H 3 9 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 0.011510 0.006645 0.000000 0.00000 SCALE2 0.000000 0.013291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009928 0.00000