PDB Short entry for 1VYM HEADER DNA BINDING PROTEIN 03-MAY-04 1VYM TITLE NATIVE HUMAN PCNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLIFERATING CELL NUCLEAR ANTIGEN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PCNA, CYCLIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DNA, REPLICATION, PROCESSIVITY, ONCOGENE, DNA-BINDING PROTEIN, DNA KEYWDS 2 REPLICATION, DNA-BINDING SYSTEMIC LUPUS ERYTHEMATOSUS, DNA BINDING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.KONTOPIDIS,S.WU,D.ZHELEVA,P.TAYLOR,C.MCINNES,D.LANE,P.FISCHER, AUTHOR 2 M.WALKINSHAW REVDAT 4 13-DEC-23 1VYM 1 REMARK REVDAT 3 24-FEB-09 1VYM 1 VERSN REVDAT 2 16-FEB-05 1VYM 1 JRNL REVDAT 1 13-JAN-05 1VYM 0 JRNL AUTH G.KONTOPIDIS,S.WU,D.ZHELEVA,P.TAYLOR,C.MCINNES,D.LANE, JRNL AUTH 2 P.FISCHER,M.WALKINSHAW JRNL TITL STRUCTURAL AND BIOCHEMICAL STUDIES OF HUMAN PROLIFERATING JRNL TITL 2 CELL NUCLEAR ANTIGEN COMPLEXES PROVIDE A RATIONALE FOR JRNL TITL 3 CYCLIN ASSOCIATION AND INHIBITOR DESIGN JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 1871 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15681588 JRNL DOI 10.1073/PNAS.0406540102 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 22893 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1274 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : -1.07000 REMARK 3 B33 (A**2) : -0.85000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.56000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.440 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.292 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.210 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.520 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VYM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1290015057. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31758 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 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: PDB ENTRY 1AXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M MAGNESIUM ACETATE, REMARK 280 PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 68.32500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.63250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.32500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 41.63250 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B2043 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THIS PROTEIN IS AN AUXILIARY PROTEIN OF DNA POLYMERASE REMARK 400 DELTA AND IS INVOLVED IN THE CONTROL OF EUKARYOTIC DNA REMARK 400 REPLICATION BY INCREASING THE POLYMERASE'S PROCESSIBILITY REMARK 400 DURING ELONGATION OF THE LEADING STRAND. 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 ASP A 257 REMARK 465 GLU A 258 REMARK 465 GLU A 259 REMARK 465 GLY A 260 REMARK 465 SER A 261 REMARK 465 ASP B 257 REMARK 465 GLU B 258 REMARK 465 GLU B 259 REMARK 465 GLY B 260 REMARK 465 SER B 261 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 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 256 CA C O CB CG CD OE1 REMARK 470 GLU A 256 OE2 REMARK 470 GLU B 256 CA C O CB CG CD OE1 REMARK 470 GLU B 256 OE2 REMARK 470 GLU C 256 CA C O CB CG CD OE1 REMARK 470 GLU C 256 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN B 125 OE1 GLU C 93 1545 1.89 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 ASP A 29 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 41 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 63 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 97 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 120 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 156 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 243 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP C 63 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP C 94 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP C 97 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 MET C 139 CG - SD - CE ANGL. DEV. = -9.6 DEGREES REMARK 500 ASP C 150 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP C 156 CB - CG - OD2 ANGL. DEV. = 6.2 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 43 -3.12 171.50 REMARK 500 ARG A 64 111.74 -171.36 REMARK 500 ALA A 67 78.39 -119.10 REMARK 500 CYS A 81 0.96 -64.61 REMARK 500 ASP A 94 -76.23 -91.49 REMARK 500 GLN A 108 61.58 -26.72 REMARK 500 LYS A 117 -73.83 -48.82 REMARK 500 LEU A 118 53.49 90.61 REMARK 500 VAL A 123 -155.76 -139.51 REMARK 500 GLN A 125 90.93 -178.47 REMARK 500 LEU A 126 -87.19 -92.78 REMARK 500 ILE A 128 130.64 58.03 REMARK 500 SER A 186 -73.49 -101.47 REMARK 500 ASN A 187 -90.41 28.71 REMARK 500 VAL A 188 159.20 61.00 REMARK 500 ASP A 189 -59.72 106.13 REMARK 500 GLU A 192 71.54 -100.01 REMARK 500 ASP A 232 -23.69 82.37 REMARK 500 ILE A 241 77.37 -109.57 REMARK 500 ALA A 242 79.71 32.43 REMARK 500 PRO A 253 -166.37 -70.61 REMARK 500 ILE A 255 128.18 37.12 REMARK 500 ASN B 24 -70.08 -91.81 REMARK 500 VAL B 45 -65.58 -97.33 REMARK 500 ASP B 94 75.26 122.00 REMARK 500 ASN B 95 -139.44 110.42 REMARK 500 ALA B 96 122.33 -21.12 REMARK 500 ASP B 97 -166.16 57.22 REMARK 500 THR B 98 98.90 28.94 REMARK 500 GLN B 108 11.58 88.80 REMARK 500 GLU B 124 -78.13 -71.97 REMARK 500 GLN B 125 175.40 67.38 REMARK 500 LEU B 126 -49.69 139.13 REMARK 500 ILE B 128 127.63 -38.90 REMARK 500 SER B 186 -103.91 -71.24 REMARK 500 GLU B 191 132.68 -39.28 REMARK 500 GLU B 193 74.29 -154.12 REMARK 500 ALA B 194 43.15 -103.09 REMARK 500 VAL B 195 112.84 -24.42 REMARK 500 ALA B 242 73.05 46.27 REMARK 500 ASP B 243 -0.71 24.65 REMARK 500 SER C 10 -39.95 -39.25 REMARK 500 ALA C 26 149.56 -174.51 REMARK 500 ASN C 95 66.50 -109.83 REMARK 500 GLN C 108 13.91 55.18 REMARK 500 LEU C 126 -79.09 -154.31 REMARK 500 ILE C 128 153.98 65.78 REMARK 500 ASP C 165 31.41 -90.68 REMARK 500 SER C 186 -76.13 -118.25 REMARK 500 ASP C 189 83.89 67.48 REMARK 500 REMARK 500 THIS ENTRY HAS 54 RAMACHANDRAN OUTLIERS. 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 ASN A 107 GLN A 108 -149.74 REMARK 500 GLU A 109 LYS A 110 -149.60 REMARK 500 GLU A 192 GLU A 193 148.04 REMARK 500 THR B 98 LEU B 99 124.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN B 95 10.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AXC RELATED DB: PDB REMARK 900 HUMAN PCNA REMARK 900 RELATED ID: 1U76 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HPCNA BOUND TO RESIDUES 452-466 OF THEDNA REMARK 900 POLYMERASE-DELTA-P66 SUBUNIT REMARK 900 RELATED ID: 1U7B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HPCNA BOUND TO RESIDUES 331-350 OF THEFLAP REMARK 900 ENDONUCLEASE-1 (FEN1) REMARK 900 RELATED ID: 1VYJ RELATED DB: PDB REMARK 900 STRUCTURAL AND BIOCHEMICAL STUDIES OF HUMAN PCNA COMPLEXES PROVIDE REMARK 900 THE BASIS FOR ASSOCIATION WITH CDK/CYCLIN AND RATIONALE FOR REMARK 900 INHIBITOR DESIGN REMARK 900 RELATED ID: 1W60 RELATED DB: PDB REMARK 900 NATIVE HUMAN PCNA DBREF 1VYM A 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 1VYM B 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 1VYM C 1 261 UNP P12004 PCNA_HUMAN 1 261 SEQRES 1 A 261 MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE LEU LYS SEQRES 2 A 261 LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN GLU ALA SEQRES 3 A 261 CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU GLN SER SEQRES 4 A 261 MET ASP SER SER HIS VAL SER LEU VAL GLN LEU THR LEU SEQRES 5 A 261 ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP ARG ASN SEQRES 6 A 261 LEU ALA MET GLY VAL ASN LEU THR SER MET SER LYS ILE SEQRES 7 A 261 LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR LEU ARG SEQRES 8 A 261 ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL PHE GLU SEQRES 9 A 261 ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU MET LYS SEQRES 10 A 261 LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE PRO GLU SEQRES 11 A 261 GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER GLY GLU SEQRES 12 A 261 PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE GLY ASP SEQRES 13 A 261 ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL LYS PHE SEQRES 14 A 261 SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE LYS LEU SEQRES 15 A 261 SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU ALA VAL SEQRES 16 A 261 THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR PHE ALA SEQRES 17 A 261 LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR PRO LEU SEQRES 18 A 261 SER SER THR VAL THR LEU SER MET SER ALA ASP VAL PRO SEQRES 19 A 261 LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY HIS LEU SEQRES 20 A 261 LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU GLU GLY SEQRES 21 A 261 SER SEQRES 1 B 261 MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE LEU LYS SEQRES 2 B 261 LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN GLU ALA SEQRES 3 B 261 CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU GLN SER SEQRES 4 B 261 MET ASP SER SER HIS VAL SER LEU VAL GLN LEU THR LEU SEQRES 5 B 261 ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP ARG ASN SEQRES 6 B 261 LEU ALA MET GLY VAL ASN LEU THR SER MET SER LYS ILE SEQRES 7 B 261 LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR LEU ARG SEQRES 8 B 261 ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL PHE GLU SEQRES 9 B 261 ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU MET LYS SEQRES 10 B 261 LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE PRO GLU SEQRES 11 B 261 GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER GLY GLU SEQRES 12 B 261 PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE GLY ASP SEQRES 13 B 261 ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL LYS PHE SEQRES 14 B 261 SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE LYS LEU SEQRES 15 B 261 SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU ALA VAL SEQRES 16 B 261 THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR PHE ALA SEQRES 17 B 261 LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR PRO LEU SEQRES 18 B 261 SER SER THR VAL THR LEU SER MET SER ALA ASP VAL PRO SEQRES 19 B 261 LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY HIS LEU SEQRES 20 B 261 LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU GLU GLY SEQRES 21 B 261 SER SEQRES 1 C 261 MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE LEU LYS SEQRES 2 C 261 LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN GLU ALA SEQRES 3 C 261 CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU GLN SER SEQRES 4 C 261 MET ASP SER SER HIS VAL SER LEU VAL GLN LEU THR LEU SEQRES 5 C 261 ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP ARG ASN SEQRES 6 C 261 LEU ALA MET GLY VAL ASN LEU THR SER MET SER LYS ILE SEQRES 7 C 261 LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR LEU ARG SEQRES 8 C 261 ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL PHE GLU SEQRES 9 C 261 ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU MET LYS SEQRES 10 C 261 LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE PRO GLU SEQRES 11 C 261 GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER GLY GLU SEQRES 12 C 261 PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE GLY ASP SEQRES 13 C 261 ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL LYS PHE SEQRES 14 C 261 SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE LYS LEU SEQRES 15 C 261 SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU ALA VAL SEQRES 16 C 261 THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR PHE ALA SEQRES 17 C 261 LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR PRO LEU SEQRES 18 C 261 SER SER THR VAL THR LEU SER MET SER ALA ASP VAL PRO SEQRES 19 C 261 LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY HIS LEU SEQRES 20 C 261 LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU GLU GLY SEQRES 21 C 261 SER FORMUL 4 HOH *141(H2 O) HELIX 1 1 GLY A 9 ALA A 18 1 10 HELIX 2 2 GLU A 55 PHE A 57 5 3 HELIX 3 3 LEU A 72 CYS A 81 1 10 HELIX 4 4 SER A 141 SER A 152 1 12 HELIX 5 5 LEU A 209 THR A 216 1 8 HELIX 6 6 LYS A 217 SER A 222 5 6 HELIX 7 7 GLN B 8 ALA B 18 1 11 HELIX 8 8 GLU B 55 PHE B 57 5 3 HELIX 9 9 LEU B 72 CYS B 81 1 10 HELIX 10 10 SER B 141 SER B 152 1 12 HELIX 11 11 LEU B 209 THR B 216 1 8 HELIX 12 12 LYS B 217 SER B 222 5 6 HELIX 13 13 GLY C 9 ALA C 18 1 10 HELIX 14 14 GLU C 55 PHE C 57 5 3 HELIX 15 15 LEU C 72 LYS C 80 1 9 HELIX 16 16 SER C 141 GLY C 155 1 15 HELIX 17 17 LEU C 209 THR C 216 1 8 HELIX 18 18 LYS C 217 SER C 222 5 6 SHEET 1 AA 9 THR A 59 CYS A 62 0 SHEET 2 AA 9 PHE A 2 LEU A 6 -1 O GLU A 3 N ARG A 61 SHEET 3 AA 9 ILE A 87 ALA A 92 -1 O ILE A 88 N LEU A 6 SHEET 4 AA 9 LEU A 99 GLU A 104 -1 O ALA A 100 N ARG A 91 SHEET 5 AA 9 LYS A 110 MET A 116 -1 O SER A 112 N PHE A 103 SHEET 6 AA 9 GLY B 176 SER B 183 -1 O ASN B 177 N GLU A 115 SHEET 7 AA 9 GLY B 166 SER B 172 -1 O VAL B 167 N LEU B 182 SHEET 8 AA 9 ALA B 157 CYS B 162 -1 O ALA B 157 N SER B 172 SHEET 9 AA 9 VAL B 203 ALA B 208 -1 O VAL B 203 N CYS B 162 SHEET 1 AB 9 LEU A 66 ASN A 71 0 SHEET 2 AB 9 GLU A 25 SER A 31 -1 O ALA A 26 N VAL A 70 SHEET 3 AB 9 GLY A 34 MET A 40 -1 O GLY A 34 N SER A 31 SHEET 4 AB 9 SER A 46 ARG A 53 -1 O VAL A 48 N SER A 39 SHEET 5 AB 9 GLY A 245 LEU A 251 -1 O HIS A 246 N THR A 51 SHEET 6 AB 9 LEU A 235 ILE A 241 -1 O LEU A 235 N LEU A 251 SHEET 7 AB 9 THR A 224 MET A 229 -1 O THR A 226 N GLU A 238 SHEET 8 AB 9 CYS A 135 PRO A 140 -1 O CYS A 135 N MET A 229 SHEET 9 AB 9 THR A 196 MET A 199 -1 O THR A 196 N LYS A 138 SHEET 1 AC 9 GLN A 204 ALA A 208 0 SHEET 2 AC 9 ALA A 157 ALA A 163 -1 O VAL A 158 N PHE A 207 SHEET 3 AC 9 GLY A 166 GLY A 173 -1 O GLY A 166 N ALA A 163 SHEET 4 AC 9 GLY A 176 SER A 183 -1 O GLY A 176 N GLY A 173 SHEET 5 AC 9 LYS C 110 LYS C 117 -1 O VAL C 111 N LYS A 181 SHEET 6 AC 9 THR C 98 GLU C 104 -1 O LEU C 99 N MET C 116 SHEET 7 AC 9 ILE C 87 ALA C 92 -1 O ILE C 87 N GLU C 104 SHEET 8 AC 9 PHE C 2 LEU C 6 -1 O PHE C 2 N ALA C 92 SHEET 9 AC 9 THR C 59 CYS C 62 -1 O THR C 59 N ARG C 5 SHEET 1 BA 9 THR B 59 CYS B 62 0 SHEET 2 BA 9 PHE B 2 LEU B 6 -1 O GLU B 3 N ARG B 61 SHEET 3 BA 9 ILE B 87 ALA B 92 -1 O ILE B 88 N LEU B 6 SHEET 4 BA 9 LEU B 99 GLU B 104 -1 O ALA B 100 N ARG B 91 SHEET 5 BA 9 LYS B 110 MET B 116 -1 O SER B 112 N PHE B 103 SHEET 6 BA 9 GLY C 176 LEU C 182 -1 O ASN C 177 N GLU B 115 SHEET 7 BA 9 GLY C 166 GLY C 173 -1 O VAL C 167 N LEU C 182 SHEET 8 BA 9 ALA C 157 ALA C 163 -1 O ALA C 157 N SER C 172 SHEET 9 BA 9 VAL C 203 ALA C 208 -1 O VAL C 203 N CYS C 162 SHEET 1 BB 9 LEU B 66 ASN B 71 0 SHEET 2 BB 9 GLU B 25 SER B 31 -1 O ALA B 26 N VAL B 70 SHEET 3 BB 9 GLY B 34 MET B 40 -1 O GLY B 34 N SER B 31 SHEET 4 BB 9 LEU B 47 ARG B 53 -1 O VAL B 48 N SER B 39 SHEET 5 BB 9 GLY B 245 LEU B 251 -1 O HIS B 246 N THR B 51 SHEET 6 BB 9 LEU B 235 ILE B 241 -1 O LEU B 235 N LEU B 251 SHEET 7 BB 9 THR B 224 MET B 229 -1 O THR B 226 N GLU B 238 SHEET 8 BB 9 CYS B 135 PRO B 140 -1 O CYS B 135 N MET B 229 SHEET 9 BB 9 THR B 196 MET B 199 -1 O THR B 196 N LYS B 138 SHEET 1 CA 9 LEU C 66 ASN C 71 0 SHEET 2 CA 9 GLU C 25 SER C 31 -1 O ALA C 26 N VAL C 70 SHEET 3 CA 9 GLY C 34 MET C 40 -1 O GLY C 34 N SER C 31 SHEET 4 CA 9 LEU C 47 ARG C 53 -1 O VAL C 48 N SER C 39 SHEET 5 CA 9 GLY C 245 LEU C 251 -1 O HIS C 246 N THR C 51 SHEET 6 CA 9 LEU C 235 ILE C 241 -1 O LEU C 235 N LEU C 251 SHEET 7 CA 9 THR C 224 MET C 229 -1 O THR C 226 N GLU C 238 SHEET 8 CA 9 CYS C 135 PRO C 140 -1 O CYS C 135 N MET C 229 SHEET 9 CA 9 THR C 196 MET C 199 -1 O THR C 196 N LYS C 138 SSBOND 1 CYS B 135 CYS B 162 1555 1555 2.78 CRYST1 136.650 83.265 71.634 90.00 117.49 90.00 C 1 2 1 12 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 0.007318 0.000000 0.003808 0.00000 SCALE2 0.000000 0.012010 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015737 0.00000