HEADER DNA BINDING PROTEIN 26-APR-21 7EP8 TITLE CRYSTAL STRUCTURE OF PCNA FROM NEUROSPORA CRASSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLIFERATING CELL NUCLEAR ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEUROSPORA CRASSA OR74A; SOURCE 3 ORGANISM_TAXID: 367110; SOURCE 4 STRAIN: ATCC 24698; SOURCE 5 GENE: PCN, NCU09239; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DNA SLIDING CLAMP, DNA REPLICATION, DNA REPAIR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.SUNDARAM,D.VASUDEVAN REVDAT 4 29-NOV-23 7EP8 1 REMARK REVDAT 3 28-JUL-21 7EP8 1 JRNL REVDAT 2 14-JUL-21 7EP8 1 JRNL REVDAT 1 30-JUN-21 7EP8 0 JRNL AUTH P.KUMARI,R.SUNDARAM,K.MANOHAR,D.VASUDEVAN,N.ACHARYA JRNL TITL INTERDOMAIN CONNECTING LOOP AND J LOOP STRUCTURES DETERMINE JRNL TITL 2 CROSS-SPECIES COMPATIBILITY OF PCNA. JRNL REF J.BIOL.CHEM. V. 297 00911 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34175309 JRNL DOI 10.1016/J.JBC.2021.100911 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 890 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 2.0010 - 1.9500 1.00 1319 68 0.2150 0.2890 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.119 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.89000 REMARK 3 B22 (A**2) : 0.89000 REMARK 3 B33 (A**2) : -1.79000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7EP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.3.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18622 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 39.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 1.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.7.02 REMARK 200 STARTING MODEL: 5TUP REMARK 200 REMARK 200 REMARK: HEXAGONAL, REMARK 200 THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM ACETATE, 20% PEG 3350, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING 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 43.14500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.90978 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.64667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 43.14500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 24.90978 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.64667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 43.14500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 24.90978 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.64667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.81955 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 61.29333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 49.81955 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 61.29333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 49.81955 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 61.29333 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: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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: 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 SER A 58 85.28 -162.49 REMARK 500 GLU A 107 -69.63 -98.48 REMARK 500 HIS A 125 77.74 42.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 7EP8 A 1 256 UNP Q7SF71 Q7SF71_NEUCR 1 256 SEQRES 1 A 256 MET LEU GLU ALA ARG LEU GLU GLN ALA SER ILE LEU LYS SEQRES 2 A 256 LYS VAL VAL ASP ALA ILE LYS ASP LEU VAL GLN ASP CYS SEQRES 3 A 256 ASN PHE ASP CYS ASN ASP SER GLY ILE ALA LEU GLN ALA SEQRES 4 A 256 MET ASP ASN SER HIS VAL ALA LEU VAL SER MET MET LEU SEQRES 5 A 256 LYS THR GLU THR PHE SER PRO PHE ARG CYS ASP ARG ASN SEQRES 6 A 256 ILE ALA LEU GLY VAL ASN LEU THR SER LEU THR LYS VAL SEQRES 7 A 256 LEU ARG ALA ALA GLN ASN GLU ASP ILE LEU THR LEU LYS SEQRES 8 A 256 ALA GLU ASP ALA PRO ASP VAL LEU ASN LEU VAL PHE GLU SEQRES 9 A 256 SER SER GLU ASN ASP ARG ILE SER GLU TYR ASP LEU LYS SEQRES 10 A 256 LEU MET ASP ILE ASP GLN GLU HIS LEU GLY ILE PRO ASP SEQRES 11 A 256 THR GLU TYR ALA ALA THR ILE SER MET PRO SER SER GLU SEQRES 12 A 256 PHE LYS ARG ILE THR THR ASP LEU MET ALA MET SER GLU SEQRES 13 A 256 SER VAL ASN ILE GLU ALA SER LYS ASP GLY VAL LYS PHE SEQRES 14 A 256 SER CYS GLN GLY ASP ILE GLY ASN GLY SER ILE THR LEU SEQRES 15 A 256 ARG GLN HIS THR ASN VAL ASP LYS PRO SER GLU ASN ILE SEQRES 16 A 256 GLU ILE GLU LEU SER GLU PRO VAL SER LEU THR PHE SER SEQRES 17 A 256 LEU LYS TYR LEU VAL ASN PHE CYS LYS ALA SER ALA LEU SEQRES 18 A 256 SER SER THR VAL LYS ILE CYS LEU SER ASN GLU VAL PRO SEQRES 19 A 256 LEU LEU VAL GLU TYR ASN ILE SER ALA SER SER TYR LEU SEQRES 20 A 256 ARG PHE TYR LEU ALA PRO LYS ILE GLY FORMUL 2 HOH *148(H2 O) HELIX 1 AA1 ALA A 9 ALA A 18 1 10 HELIX 2 AA2 GLU A 55 PHE A 57 5 3 HELIX 3 AA3 LEU A 72 ARG A 80 1 9 HELIX 4 AA4 SER A 141 ALA A 153 1 13 HELIX 5 AA5 LYS A 190 ASN A 194 5 5 HELIX 6 AA6 LEU A 209 CYS A 216 1 8 HELIX 7 AA7 LYS A 217 SER A 219 5 3 SHEET 1 AA1 5 PHE A 60 CYS A 62 0 SHEET 2 AA1 5 LEU A 2 LEU A 6 -1 N GLU A 3 O ARG A 61 SHEET 3 AA1 5 ILE A 87 ALA A 92 -1 O ALA A 92 N LEU A 2 SHEET 4 AA1 5 VAL A 98 GLU A 104 -1 O ASN A 100 N LYS A 91 SHEET 5 AA1 5 ILE A 111 LYS A 117 -1 O SER A 112 N PHE A 103 SHEET 1 AA2 9 ILE A 66 ASN A 71 0 SHEET 2 AA2 9 ASP A 25 ASN A 31 -1 N CYS A 26 O VAL A 70 SHEET 3 AA2 9 GLY A 34 MET A 40 -1 O ALA A 36 N ASP A 29 SHEET 4 AA2 9 ALA A 46 LYS A 53 -1 O LEU A 52 N ILE A 35 SHEET 5 AA2 9 TYR A 246 LEU A 251 -1 O ARG A 248 N SER A 49 SHEET 6 AA2 9 LEU A 235 TYR A 239 -1 N TYR A 239 O LEU A 247 SHEET 7 AA2 9 THR A 224 LEU A 229 -1 N CYS A 228 O LEU A 236 SHEET 8 AA2 9 ALA A 135 PRO A 140 -1 N ILE A 137 O ILE A 227 SHEET 9 AA2 9 GLU A 196 LEU A 199 -1 O GLU A 196 N SER A 138 SHEET 1 AA3 4 ASN A 177 ARG A 183 0 SHEET 2 AA3 4 GLY A 166 GLN A 172 -1 N VAL A 167 O LEU A 182 SHEET 3 AA3 4 SER A 157 ALA A 162 -1 N ASN A 159 O SER A 170 SHEET 4 AA3 4 VAL A 203 SER A 208 -1 O LEU A 205 N ILE A 160 CISPEP 1 SER A 58 PRO A 59 0 -2.59 CRYST1 86.290 86.290 91.940 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 0.011589 0.006691 0.000000 0.00000 SCALE2 0.000000 0.013382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010877 0.00000