HEADER DNA BINDING PROTEIN 18-OCT-00 1GE8 TITLE PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) HOMOLOG FROM PYROCOCCUS TITLE 2 FURIOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLIFERATION CELL NUCLEAR ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS DNA, REPLICATION, PROCESSIVITY, SLIDING CLAMP, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.MATSUMIYA,Y.ISHINO,K.MORIKAWA REVDAT 5 27-DEC-23 1GE8 1 REMARK REVDAT 4 10-NOV-21 1GE8 1 SEQADV REVDAT 3 24-FEB-09 1GE8 1 VERSN REVDAT 2 21-JAN-03 1GE8 1 REMARK REVDAT 1 24-JAN-01 1GE8 0 JRNL AUTH S.MATSUMIYA,Y.ISHINO,K.MORIKAWA JRNL TITL CRYSTAL STRUCTURE OF AN ARCHAEAL DNA SLIDING CLAMP: JRNL TITL 2 PROLIFERATING CELL NUCLEAR ANTIGEN FROM PYROCOCCUS FURIOSUS. JRNL REF PROTEIN SCI. V. 10 17 2001 JRNL REFN ISSN 0961-8368 JRNL PMID 11266590 JRNL DOI 10.1110/PS.36401 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1814731.210 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17008 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1717 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2898 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 349 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1872 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.97000 REMARK 3 B22 (A**2) : 0.97000 REMARK 3 B33 (A**2) : -1.95000 REMARK 3 B12 (A**2) : 1.50000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.680 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.110 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.600 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.590 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 57.77 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GE8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-00. REMARK 100 THE DEPOSITION ID IS D_1000005068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-00 REMARK 200 TEMPERATURE (KELVIN) : 296 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUAMTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19669 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 24.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, 1,4-DIOXANE, SODIUM REMARK 280 CITRATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+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 -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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.63450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.63450 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.63450 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HOMOTRIMER GENERATED BY THE REMARK 300 CRYSTALLOGRAPHIC THREE-FOLD AXIS. 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 BIOMT1 2 -0.500000 -0.866025 0.000000 44.84100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 77.66689 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -44.84100 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 77.66689 REMARK 350 BIOMT3 3 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 MET A 1 REMARK 465 VAL A 118 REMARK 465 GLU A 119 REMARK 465 GLU A 120 REMARK 465 MET A 121 REMARK 465 GLU A 122 REMARK 465 VAL A 123 REMARK 465 ASP A 124 REMARK 465 LEU A 125 REMARK 465 GLU A 248 REMARK 465 GLU A 249 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 ASN A 97 46.00 -83.64 REMARK 500 ASP A 235 -20.83 58.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 1GE8 A 1 249 UNP O73947 PCNA_PYRFU 1 249 SEQADV 1GE8 LEU A 73 UNP O73947 MET 73 ENGINEERED MUTATION SEQRES 1 A 249 MET PRO PHE GLU ILE VAL PHE GLU GLY ALA LYS GLU PHE SEQRES 2 A 249 ALA GLN LEU ILE ASP THR ALA SER LYS LEU ILE ASP GLU SEQRES 3 A 249 ALA ALA PHE LYS VAL THR GLU ASP GLY ILE SER MET ARG SEQRES 4 A 249 ALA MET ASP PRO SER ARG VAL VAL LEU ILE ASP LEU ASN SEQRES 5 A 249 LEU PRO SER SER ILE PHE SER LYS TYR GLU VAL VAL GLU SEQRES 6 A 249 PRO GLU THR ILE GLY VAL ASN LEU ASP HIS LEU LYS LYS SEQRES 7 A 249 ILE LEU LYS ARG GLY LYS ALA LYS ASP THR LEU ILE LEU SEQRES 8 A 249 LYS LYS GLY GLU GLU ASN PHE LEU GLU ILE THR ILE GLN SEQRES 9 A 249 GLY THR ALA THR ARG THR PHE ARG VAL PRO LEU ILE ASP SEQRES 10 A 249 VAL GLU GLU MET GLU VAL ASP LEU PRO GLU LEU PRO PHE SEQRES 11 A 249 THR ALA LYS VAL VAL VAL LEU GLY GLU VAL LEU LYS ASP SEQRES 12 A 249 ALA VAL LYS ASP ALA SER LEU VAL SER ASP SER ILE LYS SEQRES 13 A 249 PHE ILE ALA ARG GLU ASN GLU PHE ILE MET LYS ALA GLU SEQRES 14 A 249 GLY GLU THR GLN GLU VAL GLU ILE LYS LEU THR LEU GLU SEQRES 15 A 249 ASP GLU GLY LEU LEU ASP ILE GLU VAL GLN GLU GLU THR SEQRES 16 A 249 LYS SER ALA TYR GLY VAL SER TYR LEU SER ASP MET VAL SEQRES 17 A 249 LYS GLY LEU GLY LYS ALA ASP GLU VAL THR ILE LYS PHE SEQRES 18 A 249 GLY ASN GLU MET PRO MET GLN MET GLU TYR TYR ILE ARG SEQRES 19 A 249 ASP GLU GLY ARG LEU THR PHE LEU LEU ALA PRO ARG VAL SEQRES 20 A 249 GLU GLU FORMUL 2 HOH *41(H2 O) HELIX 1 1 GLY A 9 LYS A 22 1 14 HELIX 2 2 SER A 56 PHE A 58 5 3 HELIX 3 3 LEU A 73 LYS A 81 1 9 HELIX 4 4 GLY A 138 LEU A 150 1 13 HELIX 5 5 VAL A 201 VAL A 208 1 8 SHEET 1 A 5 LYS A 60 VAL A 63 0 SHEET 2 A 5 PHE A 3 GLU A 8 -1 N GLU A 4 O GLU A 62 SHEET 3 A 5 THR A 88 LYS A 93 -1 N LEU A 89 O PHE A 7 SHEET 4 A 5 PHE A 98 GLN A 104 -1 N GLU A 100 O LYS A 92 SHEET 5 A 5 THR A 108 PRO A 114 -1 O ARG A 109 N ILE A 103 SHEET 1 B 9 GLU A 67 ASN A 72 0 SHEET 2 B 9 GLU A 26 VAL A 31 -1 O ALA A 27 N VAL A 71 SHEET 3 B 9 GLY A 35 MET A 41 -1 O SER A 37 N LYS A 30 SHEET 4 B 9 VAL A 47 PRO A 54 -1 N ILE A 49 O ALA A 40 SHEET 5 B 9 GLY A 237 LEU A 243 -1 N ARG A 238 O ASN A 52 SHEET 6 B 9 MET A 227 ILE A 233 -1 O MET A 227 N LEU A 243 SHEET 7 B 9 GLU A 216 PHE A 221 -1 N THR A 218 O GLU A 230 SHEET 8 B 9 ALA A 132 LEU A 137 -1 O ALA A 132 N PHE A 221 SHEET 9 B 9 LEU A 186 VAL A 191 -1 N LEU A 187 O VAL A 135 SHEET 1 C 4 GLU A 174 THR A 180 0 SHEET 2 C 4 GLU A 163 GLU A 169 -1 N PHE A 164 O LEU A 179 SHEET 3 C 4 SER A 154 ARG A 160 -1 N LYS A 156 O LYS A 167 SHEET 4 C 4 THR A 195 GLY A 200 -1 O THR A 195 N ALA A 159 CRYST1 89.682 89.682 63.269 90.00 90.00 120.00 P 63 6 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 0.011151 0.006438 0.000000 0.00000 SCALE2 0.000000 0.012875 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015806 0.00000