HEADER DNA BINDING PROTEIN 14-JAN-19 6QH1 TITLE THE STRUCTURE OF SCHIZOSACCHAROMYCES POMBE PCNA IN COMPLEX WITH AN TITLE 2 SPD1 DERIVED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLIFERATING CELL NUCLEAR ANTIGEN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PCNA; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: S-PHASE DELAYING PROTEIN 1; COMPND 8 CHAIN: D; COMPND 9 SYNONYM: PROTEIN P14; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: PCN1, PCN, SPBC16D10.09; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 11 ORGANISM_COMMON: FISSION YEAST; SOURCE 12 ORGANISM_TAXID: 4896 KEYWDS DNA REPAIR, DNA REPLICATION, CELL CYCLE REGULATION, PCNA-SPD1 KEYWDS 2 COMPLEX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.B.KRAGELUND,O.NIELSEN,J.G.OLSEN,N.KASSEM,A.PRESTEL REVDAT 3 24-JAN-24 6QH1 1 REMARK REVDAT 2 23-JUN-21 6QH1 1 REMARK REVDAT 1 05-FEB-20 6QH1 0 JRNL AUTH B.B.KRAGELUND,J.G.OLSEN,N.KASSEM,A.PRESTEL JRNL TITL THE STRUCTURE OF SCHIZOSACCHAROMYCES POMBE PCNA IN COMPLEX JRNL TITL 2 WITH AN SPD1 DERIVED PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 18195 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 + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 980 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1326 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.3950 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5797 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -1.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.32000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.437 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.457 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.551 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5861 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5721 ; 0.009 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7917 ; 1.889 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13185 ; 1.878 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 736 ; 6.947 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 258 ;41.908 ;25.504 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1086 ;18.653 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.736 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 958 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6533 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1217 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2974 ; 5.249 ; 7.706 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2973 ; 5.244 ; 7.705 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3700 ; 8.535 ;11.557 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3701 ; 8.535 ;11.558 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2887 ; 6.896 ; 8.668 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2888 ; 6.895 ; 8.669 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4218 ;11.388 ;12.642 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 22644 ;16.998 ;73.325 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 22644 ;16.998 ;73.325 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 253 B 1 253 27368 0.14 0.05 REMARK 3 2 A 2 253 C 2 253 26420 0.15 0.05 REMARK 3 3 B 2 253 C 2 253 26928 0.15 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6QH1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8729 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19183 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 75.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 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) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 3WGW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL PH 7.5, 18% (W/V) REMARK 280 PEG4000 AND 6% (V/V) GLYCEROL, IN THE PRESENCE OF 1.9 MM SPD1(27- REMARK 280 46). [PCNA]=0.17 MM (5 MG/ML), PH 7.4, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K 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 35.82500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 LYS A 107 REMARK 465 ASN A 108 REMARK 465 GLN A 123 REMARK 465 GLU A 124 REMARK 465 HIS A 125 REMARK 465 LEU A 126 REMARK 465 LEU A 188 REMARK 465 SER A 189 REMARK 465 ASP A 190 REMARK 465 GLN A 191 REMARK 465 ILE A 254 REMARK 465 GLY A 255 REMARK 465 GLU A 256 REMARK 465 GLU A 257 REMARK 465 ASP A 258 REMARK 465 GLU A 259 REMARK 465 GLU A 260 REMARK 465 SER B 189 REMARK 465 ASP B 190 REMARK 465 ILE B 254 REMARK 465 GLY B 255 REMARK 465 GLU B 256 REMARK 465 GLU B 257 REMARK 465 ASP B 258 REMARK 465 GLU B 259 REMARK 465 GLU B 260 REMARK 465 MET C 1 REMARK 465 LYS C 107 REMARK 465 ASN C 108 REMARK 465 THR C 186 REMARK 465 ASP C 187 REMARK 465 LEU C 188 REMARK 465 SER C 189 REMARK 465 ASP C 190 REMARK 465 GLN C 191 REMARK 465 ASP C 192 REMARK 465 GLN C 193 REMARK 465 ILE C 254 REMARK 465 GLY C 255 REMARK 465 GLU C 256 REMARK 465 GLU C 257 REMARK 465 ASP C 258 REMARK 465 GLU C 259 REMARK 465 GLU C 260 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU C 199 CG CD1 CD2 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 OE1 GLU B 21 NZ LYS B 217 1.39 REMARK 500 NH2 ARG B 5 OE1 GLU B 106 1.53 REMARK 500 NH2 ARG B 5 CD2 LEU B 87 1.66 REMARK 500 OE1 GLU B 21 CE LYS B 217 1.78 REMARK 500 CZ PHE B 6 CE1 PHE B 57 1.84 REMARK 500 OE1 GLU C 21 CE LYS C 217 1.88 REMARK 500 CD2 LEU B 87 OE1 GLU B 106 1.90 REMARK 500 CE1 PHE B 6 CE1 PHE B 57 1.91 REMARK 500 CZ PHE B 6 CZ PHE B 57 1.95 REMARK 500 CE1 PHE B 6 CZ PHE B 57 1.96 REMARK 500 CD GLU B 21 NZ LYS B 217 2.06 REMARK 500 O ASN C 31 OH TYR C 60 2.08 REMARK 500 OE1 GLU C 21 NZ LYS C 217 2.09 REMARK 500 CG GLN A 83 NH2 ARG A 110 2.11 REMARK 500 NZ LYS C 13 O ALA C 82 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 224 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 224 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 MET A 241 CG - SD - CE ANGL. DEV. = 15.0 DEGREES REMARK 500 LYS B 217 CD - CE - NZ ANGL. DEV. = 16.6 DEGREES REMARK 500 MET B 229 CG - SD - CE ANGL. DEV. = 13.7 DEGREES REMARK 500 ASP C 63 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP C 63 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG C 110 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG C 110 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ILE C 131 CB - CA - C ANGL. DEV. = -13.4 DEGREES 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 SER A 243 41.53 71.23 REMARK 500 GLU B 58 -68.85 -93.01 REMARK 500 PRO B 59 77.38 -104.42 REMARK 500 HIS B 185 131.09 -175.82 REMARK 500 ALA B 222 136.34 -170.18 REMARK 500 SER B 243 38.74 73.71 REMARK 500 GLU C 58 -69.81 -91.34 REMARK 500 PRO C 59 79.46 -104.60 REMARK 500 PRO C 129 107.54 -54.91 REMARK 500 ILE C 131 -175.37 -172.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 95 PRO A 96 -39.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 6QH1 A 1 260 UNP Q03392 PCNA_SCHPO 1 260 DBREF 6QH1 B 1 260 UNP Q03392 PCNA_SCHPO 1 260 DBREF 6QH1 C 1 260 UNP Q03392 PCNA_SCHPO 1 260 DBREF 6QH1 D 29 38 UNP Q10585 SPD1_SCHPO 29 38 SEQRES 1 A 260 MET LEU GLU ALA ARG PHE GLN GLN ALA ALA LEU LEU LYS SEQRES 2 A 260 LYS LEU LEU ASP ALA ILE LYS GLU LEU VAL THR ASP ALA SEQRES 3 A 260 ASN PHE ASP CYS ASN ASP ASN GLY ILE SER LEU GLN ALA SEQRES 4 A 260 MET ASP SER SER HIS VAL ALA LEU VAL SER MET LEU ILE SEQRES 5 A 260 LYS SER ASP GLY PHE GLU PRO TYR ARG CYS ASP ARG ASN SEQRES 6 A 260 ILE ALA LEU GLY ILE ASN LEU ASN ALA LEU SER LYS VAL SEQRES 7 A 260 LEU ARG CYS ALA GLN ASN GLU ASP LEU VAL THR LEU LYS SEQRES 8 A 260 ALA GLU ASP THR PRO GLU VAL LEU ASN LEU VAL PHE GLU SEQRES 9 A 260 SER GLU LYS ASN ASP ARG ILE SER ASP TYR ASP VAL LYS SEQRES 10 A 260 LEU MET ASP ILE ASP GLN GLU HIS LEU GLY ILE PRO ASP SEQRES 11 A 260 ILE GLU TYR ASP ALA THR ILE THR MET PRO ALA ALA GLU SEQRES 12 A 260 PHE GLN ARG ILE THR ARG ASP LEU LEU THR LEU SER ASP SEQRES 13 A 260 SER VAL THR ILE ASN ALA SER LYS GLU GLY VAL ARG PHE SEQRES 14 A 260 SER CYS LYS GLY ASP ILE GLY ASN GLY SER THR THR LEU SEQRES 15 A 260 LYS GLN HIS THR ASP LEU SER ASP GLN ASP GLN SER ILE SEQRES 16 A 260 GLU ILE SER LEU THR GLN ALA VAL THR LEU THR PHE SER SEQRES 17 A 260 LEU LYS TYR LEU ALA GLN PHE THR LYS ALA THR PRO LEU SEQRES 18 A 260 ALA THR ARG VAL THR LEU SER MET SER ASN ASP VAL PRO SEQRES 19 A 260 LEU LEU VAL GLU TYR LYS MET GLU SER GLY PHE LEU ARG SEQRES 20 A 260 PHE TYR LEU ALA PRO LYS ILE GLY GLU GLU ASP GLU GLU SEQRES 1 B 260 MET LEU GLU ALA ARG PHE GLN GLN ALA ALA LEU LEU LYS SEQRES 2 B 260 LYS LEU LEU ASP ALA ILE LYS GLU LEU VAL THR ASP ALA SEQRES 3 B 260 ASN PHE ASP CYS ASN ASP ASN GLY ILE SER LEU GLN ALA SEQRES 4 B 260 MET ASP SER SER HIS VAL ALA LEU VAL SER MET LEU ILE SEQRES 5 B 260 LYS SER ASP GLY PHE GLU PRO TYR ARG CYS ASP ARG ASN SEQRES 6 B 260 ILE ALA LEU GLY ILE ASN LEU ASN ALA LEU SER LYS VAL SEQRES 7 B 260 LEU ARG CYS ALA GLN ASN GLU ASP LEU VAL THR LEU LYS SEQRES 8 B 260 ALA GLU ASP THR PRO GLU VAL LEU ASN LEU VAL PHE GLU SEQRES 9 B 260 SER GLU LYS ASN ASP ARG ILE SER ASP TYR ASP VAL LYS SEQRES 10 B 260 LEU MET ASP ILE ASP GLN GLU HIS LEU GLY ILE PRO ASP SEQRES 11 B 260 ILE GLU TYR ASP ALA THR ILE THR MET PRO ALA ALA GLU SEQRES 12 B 260 PHE GLN ARG ILE THR ARG ASP LEU LEU THR LEU SER ASP SEQRES 13 B 260 SER VAL THR ILE ASN ALA SER LYS GLU GLY VAL ARG PHE SEQRES 14 B 260 SER CYS LYS GLY ASP ILE GLY ASN GLY SER THR THR LEU SEQRES 15 B 260 LYS GLN HIS THR ASP LEU SER ASP GLN ASP GLN SER ILE SEQRES 16 B 260 GLU ILE SER LEU THR GLN ALA VAL THR LEU THR PHE SER SEQRES 17 B 260 LEU LYS TYR LEU ALA GLN PHE THR LYS ALA THR PRO LEU SEQRES 18 B 260 ALA THR ARG VAL THR LEU SER MET SER ASN ASP VAL PRO SEQRES 19 B 260 LEU LEU VAL GLU TYR LYS MET GLU SER GLY PHE LEU ARG SEQRES 20 B 260 PHE TYR LEU ALA PRO LYS ILE GLY GLU GLU ASP GLU GLU SEQRES 1 C 260 MET LEU GLU ALA ARG PHE GLN GLN ALA ALA LEU LEU LYS SEQRES 2 C 260 LYS LEU LEU ASP ALA ILE LYS GLU LEU VAL THR ASP ALA SEQRES 3 C 260 ASN PHE ASP CYS ASN ASP ASN GLY ILE SER LEU GLN ALA SEQRES 4 C 260 MET ASP SER SER HIS VAL ALA LEU VAL SER MET LEU ILE SEQRES 5 C 260 LYS SER ASP GLY PHE GLU PRO TYR ARG CYS ASP ARG ASN SEQRES 6 C 260 ILE ALA LEU GLY ILE ASN LEU ASN ALA LEU SER LYS VAL SEQRES 7 C 260 LEU ARG CYS ALA GLN ASN GLU ASP LEU VAL THR LEU LYS SEQRES 8 C 260 ALA GLU ASP THR PRO GLU VAL LEU ASN LEU VAL PHE GLU SEQRES 9 C 260 SER GLU LYS ASN ASP ARG ILE SER ASP TYR ASP VAL LYS SEQRES 10 C 260 LEU MET ASP ILE ASP GLN GLU HIS LEU GLY ILE PRO ASP SEQRES 11 C 260 ILE GLU TYR ASP ALA THR ILE THR MET PRO ALA ALA GLU SEQRES 12 C 260 PHE GLN ARG ILE THR ARG ASP LEU LEU THR LEU SER ASP SEQRES 13 C 260 SER VAL THR ILE ASN ALA SER LYS GLU GLY VAL ARG PHE SEQRES 14 C 260 SER CYS LYS GLY ASP ILE GLY ASN GLY SER THR THR LEU SEQRES 15 C 260 LYS GLN HIS THR ASP LEU SER ASP GLN ASP GLN SER ILE SEQRES 16 C 260 GLU ILE SER LEU THR GLN ALA VAL THR LEU THR PHE SER SEQRES 17 C 260 LEU LYS TYR LEU ALA GLN PHE THR LYS ALA THR PRO LEU SEQRES 18 C 260 ALA THR ARG VAL THR LEU SER MET SER ASN ASP VAL PRO SEQRES 19 C 260 LEU LEU VAL GLU TYR LYS MET GLU SER GLY PHE LEU ARG SEQRES 20 C 260 PHE TYR LEU ALA PRO LYS ILE GLY GLU GLU ASP GLU GLU SEQRES 1 D 10 ILE GLN GLY SER LEU MET ASP VAL GLY MET HELIX 1 AA1 ALA A 9 GLU A 21 1 13 HELIX 2 AA2 ASP A 55 PHE A 57 5 3 HELIX 3 AA3 LEU A 72 ARG A 80 1 9 HELIX 4 AA4 ALA A 141 SER A 155 1 15 HELIX 5 AA5 LEU A 209 THR A 216 1 8 HELIX 6 AA6 LYS A 217 ALA A 222 5 6 HELIX 7 AA7 ALA B 9 GLU B 21 1 13 HELIX 8 AA8 ASP B 55 PHE B 57 5 3 HELIX 9 AA9 LEU B 72 ARG B 80 1 9 HELIX 10 AB1 ALA B 141 SER B 155 1 15 HELIX 11 AB2 LEU B 209 THR B 216 1 8 HELIX 12 AB3 LYS B 217 ALA B 222 5 6 HELIX 13 AB4 ALA C 9 GLU C 21 1 13 HELIX 14 AB5 ASP C 55 PHE C 57 5 3 HELIX 15 AB6 LEU C 72 ARG C 80 1 9 HELIX 16 AB7 ALA C 141 SER C 155 1 15 HELIX 17 AB8 LEU C 209 THR C 216 1 8 HELIX 18 AB9 LYS C 217 ALA C 222 5 6 HELIX 19 AC1 SER D 32 GLY D 37 5 6 SHEET 1 AA1 9 TYR A 60 CYS A 62 0 SHEET 2 AA1 9 LEU A 2 ARG A 5 -1 N GLU A 3 O ARG A 61 SHEET 3 AA1 9 LEU A 87 ALA A 92 -1 O LEU A 90 N ALA A 4 SHEET 4 AA1 9 VAL A 98 SER A 105 -1 O ASN A 100 N LYS A 91 SHEET 5 AA1 9 ARG A 110 LYS A 117 -1 O VAL A 116 N LEU A 99 SHEET 6 AA1 9 GLY B 176 LEU B 182 -1 O ASN B 177 N ASP A 115 SHEET 7 AA1 9 GLY B 166 LYS B 172 -1 N VAL B 167 O LEU B 182 SHEET 8 AA1 9 SER B 157 SER B 163 -1 N THR B 159 O SER B 170 SHEET 9 AA1 9 VAL B 203 SER B 208 -1 O LEU B 205 N ILE B 160 SHEET 1 AA2 9 ILE A 66 ASN A 71 0 SHEET 2 AA2 9 ASP A 25 CYS A 30 -1 N CYS A 30 O ILE A 66 SHEET 3 AA2 9 GLY A 34 MET A 40 -1 O SER A 36 N ASP A 29 SHEET 4 AA2 9 ALA A 46 LYS A 53 -1 O VAL A 48 N ALA A 39 SHEET 5 AA2 9 GLY A 244 LEU A 250 -1 O TYR A 249 N LEU A 47 SHEET 6 AA2 9 VAL A 233 MET A 241 -1 N VAL A 237 O PHE A 248 SHEET 7 AA2 9 ARG A 224 SER A 230 -1 N THR A 226 O GLU A 238 SHEET 8 AA2 9 ALA A 135 PRO A 140 -1 N MET A 139 O VAL A 225 SHEET 9 AA2 9 GLU A 196 LEU A 199 -1 O GLU A 196 N THR A 138 SHEET 1 AA3 8 VAL A 203 SER A 208 0 SHEET 2 AA3 8 SER A 157 SER A 163 -1 N ILE A 160 O LEU A 205 SHEET 3 AA3 8 GLY A 166 SER A 170 -1 O SER A 170 N THR A 159 SHEET 4 AA3 8 GLY A 176 LEU A 182 -1 O LEU A 182 N VAL A 167 SHEET 5 AA3 8 ILE C 111 LYS C 117 -1 O ASP C 113 N SER A 179 SHEET 6 AA3 8 VAL C 98 GLU C 104 -1 N LEU C 99 O VAL C 116 SHEET 7 AA3 8 LEU C 87 LYS C 91 -1 N LEU C 87 O GLU C 104 SHEET 8 AA3 8 GLU C 3 ARG C 5 -1 N ALA C 4 O LEU C 90 SHEET 1 AA4 9 ARG B 61 CYS B 62 0 SHEET 2 AA4 9 LEU B 2 PHE B 6 -1 N GLU B 3 O ARG B 61 SHEET 3 AA4 9 LEU B 87 ALA B 92 -1 O LEU B 90 N ALA B 4 SHEET 4 AA4 9 VAL B 98 GLU B 104 -1 O ASN B 100 N LYS B 91 SHEET 5 AA4 9 ARG B 110 LYS B 117 -1 O VAL B 116 N LEU B 99 SHEET 6 AA4 9 GLY C 176 LEU C 182 -1 O SER C 179 N ASP B 113 SHEET 7 AA4 9 GLY C 166 LYS C 172 -1 N CYS C 171 O GLY C 178 SHEET 8 AA4 9 SER C 157 SER C 163 -1 N THR C 159 O SER C 170 SHEET 9 AA4 9 VAL C 203 SER C 208 -1 O LEU C 205 N ILE C 160 SHEET 1 AA5 9 ILE B 66 ASN B 71 0 SHEET 2 AA5 9 ASP B 25 CYS B 30 -1 N CYS B 30 O ILE B 66 SHEET 3 AA5 9 GLY B 34 MET B 40 -1 O SER B 36 N ASP B 29 SHEET 4 AA5 9 ALA B 46 LYS B 53 -1 O ILE B 52 N ILE B 35 SHEET 5 AA5 9 GLY B 244 LEU B 250 -1 O ARG B 247 N SER B 49 SHEET 6 AA5 9 VAL B 233 MET B 241 -1 N VAL B 237 O PHE B 248 SHEET 7 AA5 9 ARG B 224 SER B 230 -1 N THR B 226 O GLU B 238 SHEET 8 AA5 9 ALA B 135 PRO B 140 -1 N ILE B 137 O LEU B 227 SHEET 9 AA5 9 GLU B 196 LEU B 199 -1 O GLU B 196 N THR B 138 SHEET 1 AA6 9 ILE C 66 ASN C 71 0 SHEET 2 AA6 9 ASP C 25 CYS C 30 -1 N CYS C 30 O ILE C 66 SHEET 3 AA6 9 GLY C 34 MET C 40 -1 O SER C 36 N ASP C 29 SHEET 4 AA6 9 ALA C 46 LYS C 53 -1 O VAL C 48 N ALA C 39 SHEET 5 AA6 9 GLY C 244 LEU C 250 -1 O TYR C 249 N LEU C 47 SHEET 6 AA6 9 VAL C 233 MET C 241 -1 N VAL C 237 O PHE C 248 SHEET 7 AA6 9 ARG C 224 SER C 230 -1 N THR C 226 O GLU C 238 SHEET 8 AA6 9 ALA C 135 PRO C 140 -1 N ILE C 137 O LEU C 227 SHEET 9 AA6 9 GLU C 196 LEU C 199 -1 O GLU C 196 N THR C 138 CISPEP 1 THR B 95 PRO B 96 0 -20.87 CISPEP 2 LYS B 107 ASN B 108 0 5.10 CRYST1 80.860 71.650 84.020 90.00 115.75 90.00 P 1 21 1 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 0.012367 0.000000 0.005965 0.00000 SCALE2 0.000000 0.013957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013214 0.00000