HEADER REPLICATION 25-DEC-18 6QC0 TITLE PCNA COMPLEX WITH CDT2 C-TERMINAL PIP-BOX PEPTIDE CAVEAT 6QC0 SER A 186 HAS WRONG CHIRALITY AT ATOM CA ASP E 122 HAS WRONG CAVEAT 2 6QC0 CHIRALITY AT ATOM CA VAL E 188 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 6QC0 CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLIFERATING CELL NUCLEAR ANTIGEN; COMPND 3 CHAIN: A, C, E; COMPND 4 SYNONYM: PCNA,CYCLIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DENTICLELESS PROTEIN HOMOLOG; COMPND 8 CHAIN: B, D, F; COMPND 9 SYNONYM: DDB1- AND CUL4-ASSOCIATED FACTOR 2,LETHAL(2) DENTICLELESS COMPND 10 PROTEIN HOMOLOG,RETINOIC ACID-REGULATED NUCLEAR MATRIX-ASSOCIATED COMPND 11 PROTEIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PCNA; 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: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS COMPLEX, PIP, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR A.P.PERRAKIS,E.VON CASTELMUR REVDAT 1 23-JAN-19 6QC0 0 JRNL AUTH A.HAYASHI,N.N.GIAKOUMAKIS,T.HEIDEBRECHT,T.ISHII, JRNL AUTH 2 A.PANAGOPOULOS,C.CAILLAT,M.TAKAHARA,R.G.HIBBERT,N.SUENAGA, JRNL AUTH 3 M.STADNIK-SPIEWAK,T.TAKAHASHI,Y.SHIOMI,S.TARAVIRAS, JRNL AUTH 4 E.VON CASTELMUR,Z.LYGEROU,A.PERRAKIS,H.NISHITANI JRNL TITL DIRECT BINDING OF CDT2 TO PCNA IS IMPORTANT FOR TARGETING JRNL TITL 2 THE CRL4CDT2E3 LIGASE ACTIVITY TO CDT1. JRNL REF LIFE SCI ALLIANCE V. 1 00238 2018 JRNL REFN ESSN 2575-1077 JRNL PMID 30623174 JRNL DOI 10.26508/LSA.201800238 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 14082 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 748 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) : 3.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 659 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6173 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) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.83000 REMARK 3 B22 (A**2) : -0.83000 REMARK 3 B33 (A**2) : 2.71000 REMARK 3 B12 (A**2) : -0.42000 REMARK 3 B13 (A**2) : 0.00000 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): 0.598 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.513 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 82.844 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.856 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6256 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5923 ; 0.007 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8438 ; 1.806 ; 1.632 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13782 ; 1.272 ; 1.577 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 790 ; 9.357 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 296 ;40.697 ;23.716 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1170 ;21.156 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;24.355 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 842 ; 0.233 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6894 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1192 ; 0.005 ; 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): 3181 ; 2.069 ; 4.081 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3180 ; 2.069 ; 4.081 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3964 ; 3.615 ; 6.118 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3965 ; 3.615 ; 6.118 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3075 ; 1.762 ; 4.278 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3076 ; 1.762 ; 4.278 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4475 ; 3.181 ; 6.331 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6492 ; 6.029 ;46.675 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6493 ; 6.028 ;46.675 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 : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 255 C 1 255 6983 0.14 0.05 REMARK 3 2 A 1 255 E 1 255 6948 0.14 0.05 REMARK 3 3 C 1 255 E 1 255 7078 0.13 0.05 REMARK 3 4 B 705 715 D 705 715 243 0.15 0.05 REMARK 3 5 B 705 715 F 705 715 271 0.17 0.05 REMARK 3 6 D 705 715 F 705 715 244 0.19 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 6 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 999 REMARK 3 RESIDUE RANGE : C 0 C 999 REMARK 3 RESIDUE RANGE : E 0 E 999 REMARK 3 RESIDUE RANGE : B 0 B 999 REMARK 3 RESIDUE RANGE : D 0 D 999 REMARK 3 RESIDUE RANGE : F 0 F 999 REMARK 3 ORIGIN FOR THE GROUP (A): 41.2920 15.9880 -4.6240 REMARK 3 T TENSOR REMARK 3 T11: 0.0477 T22: 0.0369 REMARK 3 T33: 0.4358 T12: -0.0328 REMARK 3 T13: 0.0080 T23: -0.0584 REMARK 3 L TENSOR REMARK 3 L11: 1.6129 L22: 0.8321 REMARK 3 L33: 1.4987 L12: -0.4666 REMARK 3 L13: -0.1369 L23: -0.2674 REMARK 3 S TENSOR REMARK 3 S11: 0.0748 S12: -0.1151 S13: -0.0966 REMARK 3 S21: -0.0888 S22: 0.0457 S23: 0.0656 REMARK 3 S31: -0.1413 S32: 0.0757 S33: -0.1204 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 6QC0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.872600 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14850 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 6000 100 MM MES/HCL, PH REMARK 280 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 30.49633 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 60.99267 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 45.74450 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 76.24083 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 15.24817 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E, B, D, F 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 ASP A 189 REMARK 465 LYS A 190 REMARK 465 GLU A 191 REMARK 465 GLU A 258 REMARK 465 GLU A 259 REMARK 465 GLY A 260 REMARK 465 SER A 261 REMARK 465 GLY C -1 REMARK 465 PRO C 0 REMARK 465 GLU C 256 REMARK 465 ASP C 257 REMARK 465 GLU C 258 REMARK 465 GLU C 259 REMARK 465 GLY C 260 REMARK 465 SER C 261 REMARK 465 GLY E -1 REMARK 465 PRO E 0 REMARK 465 GLU E 256 REMARK 465 ASP E 257 REMARK 465 GLU E 258 REMARK 465 GLU E 259 REMARK 465 GLY E 260 REMARK 465 SER E 261 REMARK 465 SER B 704 REMARK 465 LYS B 716 REMARK 465 SER B 717 REMARK 465 SER D 704 REMARK 465 LYS D 716 REMARK 465 SER D 717 REMARK 465 SER F 704 REMARK 465 LYS F 716 REMARK 465 SER F 717 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 GLU A 192 CG CD OE1 OE2 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 OD1 ASP E 41 OG SER E 43 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 64 CZ ARG A 64 NH2 0.160 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 64 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 156 CB - CA - C ANGL. DEV. = -12.0 DEGREES REMARK 500 ASP C 156 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 ASP E 122 CB - CA - C ANGL. DEV. = 21.1 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 42 -44.68 -26.60 REMARK 500 HIS A 44 37.65 70.91 REMARK 500 GLN A 108 17.51 51.96 REMARK 500 ASP A 113 77.52 -164.82 REMARK 500 GLU A 115 118.89 -171.46 REMARK 500 GLU A 124 99.02 -61.85 REMARK 500 SER A 186 119.01 -32.88 REMARK 500 ASN A 187 126.60 58.09 REMARK 500 PRO A 220 7.55 -67.77 REMARK 500 ASP A 232 47.48 33.73 REMARK 500 ALA A 242 51.69 36.20 REMARK 500 ASP A 243 -23.28 78.35 REMARK 500 PRO A 253 -153.85 -75.77 REMARK 500 LYS A 254 -107.74 -127.86 REMARK 500 ILE A 255 128.17 69.38 REMARK 500 GLU A 256 -122.06 -88.40 REMARK 500 SER C 42 -43.83 -24.43 REMARK 500 ASP C 113 78.01 -166.23 REMARK 500 GLU C 124 99.26 -68.75 REMARK 500 VAL C 188 95.94 -39.64 REMARK 500 PRO C 220 7.57 -67.45 REMARK 500 ALA C 242 54.27 35.03 REMARK 500 ASP C 243 -26.19 80.79 REMARK 500 PRO C 253 -148.62 -76.73 REMARK 500 LYS C 254 -145.97 -127.98 REMARK 500 SER E 42 -42.87 -29.58 REMARK 500 ASP E 113 79.52 -166.95 REMARK 500 GLU E 115 120.69 -170.59 REMARK 500 VAL E 188 91.24 -27.92 REMARK 500 LYS E 190 -143.52 -128.66 REMARK 500 PRO E 220 8.85 -68.52 REMARK 500 ASP E 232 50.40 29.53 REMARK 500 ALA E 242 49.80 37.45 REMARK 500 ASP E 243 -21.43 78.41 REMARK 500 PRO E 253 -155.77 -77.29 REMARK 500 MET B 706 133.18 117.75 REMARK 500 PHE B 713 -101.08 -130.85 REMARK 500 HIS B 714 111.02 81.03 REMARK 500 MET D 706 125.17 123.55 REMARK 500 ARG D 707 -169.15 -103.72 REMARK 500 PHE D 713 -102.73 -129.79 REMARK 500 HIS D 714 137.73 77.55 REMARK 500 PHE F 713 -108.32 -132.36 REMARK 500 HIS F 714 112.81 72.14 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 GLU A 109 LYS A 110 149.81 REMARK 500 THR A 185 SER A 186 143.44 REMARK 500 GLU A 193 ALA A 194 -144.42 REMARK 500 ASN C 107 GLN C 108 148.95 REMARK 500 ASN C 187 VAL C 188 -148.87 REMARK 500 VAL C 188 ASP C 189 -138.70 REMARK 500 LYS C 190 GLU C 191 -141.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 6QC0 A 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 6QC0 C 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 6QC0 E 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 6QC0 B 704 717 UNP Q9NZJ0 DTL_HUMAN 704 717 DBREF 6QC0 D 704 717 UNP Q9NZJ0 DTL_HUMAN 704 717 DBREF 6QC0 F 704 717 UNP Q9NZJ0 DTL_HUMAN 704 717 SEQADV 6QC0 GLY A -1 UNP P12004 EXPRESSION TAG SEQADV 6QC0 PRO A 0 UNP P12004 EXPRESSION TAG SEQADV 6QC0 GLY C -1 UNP P12004 EXPRESSION TAG SEQADV 6QC0 PRO C 0 UNP P12004 EXPRESSION TAG SEQADV 6QC0 GLY E -1 UNP P12004 EXPRESSION TAG SEQADV 6QC0 PRO E 0 UNP P12004 EXPRESSION TAG SEQRES 1 A 263 GLY PRO MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE SEQRES 2 A 263 LEU LYS LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN SEQRES 3 A 263 GLU ALA CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU SEQRES 4 A 263 GLN SER MET ASP SER SER HIS VAL SER LEU VAL GLN LEU SEQRES 5 A 263 THR LEU ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP SEQRES 6 A 263 ARG ASN LEU ALA MET GLY VAL ASN LEU THR SER MET SER SEQRES 7 A 263 LYS ILE LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR SEQRES 8 A 263 LEU ARG ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL SEQRES 9 A 263 PHE GLU ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU SEQRES 10 A 263 MET LYS LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE SEQRES 11 A 263 PRO GLU GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER SEQRES 12 A 263 GLY GLU PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE SEQRES 13 A 263 GLY ASP ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL SEQRES 14 A 263 LYS PHE SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE SEQRES 15 A 263 LYS LEU SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU SEQRES 16 A 263 ALA VAL THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR SEQRES 17 A 263 PHE ALA LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR SEQRES 18 A 263 PRO LEU SER SER THR VAL THR LEU SER MET SER ALA ASP SEQRES 19 A 263 VAL PRO LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY SEQRES 20 A 263 HIS LEU LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU SEQRES 21 A 263 GLU GLY SER SEQRES 1 C 263 GLY PRO MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE SEQRES 2 C 263 LEU LYS LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN SEQRES 3 C 263 GLU ALA CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU SEQRES 4 C 263 GLN SER MET ASP SER SER HIS VAL SER LEU VAL GLN LEU SEQRES 5 C 263 THR LEU ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP SEQRES 6 C 263 ARG ASN LEU ALA MET GLY VAL ASN LEU THR SER MET SER SEQRES 7 C 263 LYS ILE LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR SEQRES 8 C 263 LEU ARG ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL SEQRES 9 C 263 PHE GLU ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU SEQRES 10 C 263 MET LYS LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE SEQRES 11 C 263 PRO GLU GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER SEQRES 12 C 263 GLY GLU PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE SEQRES 13 C 263 GLY ASP ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL SEQRES 14 C 263 LYS PHE SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE SEQRES 15 C 263 LYS LEU SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU SEQRES 16 C 263 ALA VAL THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR SEQRES 17 C 263 PHE ALA LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR SEQRES 18 C 263 PRO LEU SER SER THR VAL THR LEU SER MET SER ALA ASP SEQRES 19 C 263 VAL PRO LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY SEQRES 20 C 263 HIS LEU LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU SEQRES 21 C 263 GLU GLY SER SEQRES 1 E 263 GLY PRO MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE SEQRES 2 E 263 LEU LYS LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN SEQRES 3 E 263 GLU ALA CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU SEQRES 4 E 263 GLN SER MET ASP SER SER HIS VAL SER LEU VAL GLN LEU SEQRES 5 E 263 THR LEU ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP SEQRES 6 E 263 ARG ASN LEU ALA MET GLY VAL ASN LEU THR SER MET SER SEQRES 7 E 263 LYS ILE LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR SEQRES 8 E 263 LEU ARG ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL SEQRES 9 E 263 PHE GLU ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU SEQRES 10 E 263 MET LYS LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE SEQRES 11 E 263 PRO GLU GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER SEQRES 12 E 263 GLY GLU PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE SEQRES 13 E 263 GLY ASP ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL SEQRES 14 E 263 LYS PHE SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE SEQRES 15 E 263 LYS LEU SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU SEQRES 16 E 263 ALA VAL THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR SEQRES 17 E 263 PHE ALA LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR SEQRES 18 E 263 PRO LEU SER SER THR VAL THR LEU SER MET SER ALA ASP SEQRES 19 E 263 VAL PRO LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY SEQRES 20 E 263 HIS LEU LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU SEQRES 21 E 263 GLU GLY SER SEQRES 1 B 14 SER SER MET ARG LYS ILE CYS THR TYR PHE HIS ARG LYS SEQRES 2 B 14 SER SEQRES 1 D 14 SER SER MET ARG LYS ILE CYS THR TYR PHE HIS ARG LYS SEQRES 2 D 14 SER SEQRES 1 F 14 SER SER MET ARG LYS ILE CYS THR TYR PHE HIS ARG LYS SEQRES 2 F 14 SER HELIX 1 AA1 GLN A 8 ASP A 21 1 14 HELIX 2 AA2 GLU A 55 PHE A 57 5 3 HELIX 3 AA3 LEU A 72 LYS A 80 1 9 HELIX 4 AA4 SER A 141 SER A 152 1 12 HELIX 5 AA5 LEU A 209 THR A 216 1 8 HELIX 6 AA6 LYS A 217 SER A 222 5 6 HELIX 7 AA7 GLN C 8 ASP C 21 1 14 HELIX 8 AA8 GLU C 55 PHE C 57 5 3 HELIX 9 AA9 LEU C 72 LYS C 80 1 9 HELIX 10 AB1 SER C 141 SER C 152 1 12 HELIX 11 AB2 LEU C 209 THR C 216 1 8 HELIX 12 AB3 LYS C 217 SER C 222 5 6 HELIX 13 AB4 GLN E 8 ASP E 21 1 14 HELIX 14 AB5 GLU E 55 PHE E 57 5 3 HELIX 15 AB6 LEU E 72 LYS E 80 1 9 HELIX 16 AB7 SER E 141 SER E 152 1 12 HELIX 17 AB8 LEU E 209 THR E 216 1 8 HELIX 18 AB9 LYS E 217 SER E 222 5 6 HELIX 19 AC1 LYS F 708 PHE F 713 1 6 SHEET 1 AA1 9 THR A 59 ARG A 61 0 SHEET 2 AA1 9 PHE A 2 LEU A 6 -1 N GLU A 3 O ARG A 61 SHEET 3 AA1 9 ILE A 87 ALA A 92 -1 O ALA A 92 N PHE A 2 SHEET 4 AA1 9 THR A 98 GLU A 104 -1 O VAL A 102 N THR A 89 SHEET 5 AA1 9 LYS A 110 LYS A 117 -1 O MET A 116 N LEU A 99 SHEET 6 AA1 9 GLY C 176 SER C 183 -1 O LYS C 181 N VAL A 111 SHEET 7 AA1 9 GLY C 166 SER C 172 -1 N PHE C 169 O ILE C 180 SHEET 8 AA1 9 ALA C 157 CYS C 162 -1 N VAL C 159 O SER C 170 SHEET 9 AA1 9 VAL C 203 ALA C 208 -1 O LEU C 205 N ILE C 160 SHEET 1 AA2 9 LEU A 66 ASN A 71 0 SHEET 2 AA2 9 GLU A 25 SER A 31 -1 N TRP A 28 O MET A 68 SHEET 3 AA2 9 GLY A 34 MET A 40 -1 O ASN A 36 N ASP A 29 SHEET 4 AA2 9 SER A 46 ARG A 53 -1 O LEU A 50 N LEU A 37 SHEET 5 AA2 9 GLY A 245 LEU A 251 -1 O TYR A 250 N LEU A 47 SHEET 6 AA2 9 VAL A 233 ILE A 241 -1 N VAL A 237 O TYR A 249 SHEET 7 AA2 9 THR A 224 SER A 230 -1 N THR A 226 O GLU A 238 SHEET 8 AA2 9 CYS A 135 PRO A 140 -1 N VAL A 137 O LEU A 227 SHEET 9 AA2 9 THR A 196 MET A 199 -1 O THR A 196 N LYS A 138 SHEET 1 AA3 9 VAL A 203 ALA A 208 0 SHEET 2 AA3 9 ALA A 157 CYS A 162 -1 N ILE A 160 O LEU A 205 SHEET 3 AA3 9 GLY A 166 SER A 172 -1 O SER A 170 N VAL A 159 SHEET 4 AA3 9 GLY A 176 SER A 183 -1 O ILE A 180 N PHE A 169 SHEET 5 AA3 9 LYS E 110 LYS E 117 -1 O VAL E 111 N LYS A 181 SHEET 6 AA3 9 THR E 98 GLU E 104 -1 N LEU E 99 O MET E 116 SHEET 7 AA3 9 ILE E 87 ALA E 92 -1 N THR E 89 O VAL E 102 SHEET 8 AA3 9 PHE E 2 LEU E 6 -1 N PHE E 2 O ALA E 92 SHEET 9 AA3 9 THR E 59 CYS E 62 -1 O ARG E 61 N GLU E 3 SHEET 1 AA4 9 THR C 59 CYS C 62 0 SHEET 2 AA4 9 PHE C 2 LEU C 6 -1 N GLU C 3 O ARG C 61 SHEET 3 AA4 9 ILE C 87 ALA C 92 -1 O ALA C 92 N PHE C 2 SHEET 4 AA4 9 THR C 98 GLU C 104 -1 O VAL C 102 N THR C 89 SHEET 5 AA4 9 LYS C 110 LYS C 117 -1 O MET C 116 N LEU C 99 SHEET 6 AA4 9 GLY E 176 SER E 183 -1 O LYS E 181 N VAL C 111 SHEET 7 AA4 9 GLY E 166 SER E 172 -1 N PHE E 169 O ILE E 180 SHEET 8 AA4 9 ALA E 157 CYS E 162 -1 N VAL E 159 O SER E 170 SHEET 9 AA4 9 VAL E 203 ALA E 208 -1 O LEU E 205 N ILE E 160 SHEET 1 AA5 9 LEU C 66 ASN C 71 0 SHEET 2 AA5 9 GLU C 25 SER C 31 -1 N TRP C 28 O MET C 68 SHEET 3 AA5 9 GLY C 34 MET C 40 -1 O ASN C 36 N ASP C 29 SHEET 4 AA5 9 SER C 46 ARG C 53 -1 O LEU C 50 N LEU C 37 SHEET 5 AA5 9 GLY C 245 LEU C 251 -1 O TYR C 250 N LEU C 47 SHEET 6 AA5 9 VAL C 233 ILE C 241 -1 N VAL C 237 O TYR C 249 SHEET 7 AA5 9 THR C 224 SER C 230 -1 N THR C 226 O GLU C 238 SHEET 8 AA5 9 CYS C 135 PRO C 140 -1 N VAL C 137 O LEU C 227 SHEET 9 AA5 9 THR C 196 MET C 199 -1 O THR C 196 N LYS C 138 SHEET 1 AA6 9 LEU E 66 ASN E 71 0 SHEET 2 AA6 9 GLU E 25 SER E 31 -1 N TRP E 28 O MET E 68 SHEET 3 AA6 9 GLY E 34 MET E 40 -1 O ASN E 36 N ASP E 29 SHEET 4 AA6 9 SER E 46 ARG E 53 -1 O LEU E 50 N LEU E 37 SHEET 5 AA6 9 GLY E 245 LEU E 251 -1 O TYR E 250 N LEU E 47 SHEET 6 AA6 9 VAL E 233 ILE E 241 -1 N VAL E 237 O TYR E 249 SHEET 7 AA6 9 THR E 224 SER E 230 -1 N THR E 226 O GLU E 238 SHEET 8 AA6 9 CYS E 135 PRO E 140 -1 N VAL E 137 O LEU E 227 SHEET 9 AA6 9 THR E 196 MET E 199 -1 O THR E 196 N LYS E 138 CRYST1 151.369 151.369 91.489 90.00 90.00 120.00 P 61 18 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 0.006606 0.003814 0.000000 0.00000 SCALE2 0.000000 0.007628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010930 0.00000