HEADER REPLICATION 17-MAY-19 6K3A TITLE CRYSTAL STRUCTURE OF HUMAN PCNA IN COMPLEX WITH DNMT1 PIP BOX MOTIF. 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: PEPTIDE FROM DNA (CYTOSINE-5)-METHYLTRANSFERASE 1; COMPND 8 CHAIN: B, D, F; COMPND 9 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 DNMT1, PCNA, DNA METHYLATION, PIP BOX, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR T.JIMENJI,S.KORI,K.ARITA REVDAT 4 22-NOV-23 6K3A 1 REMARK REVDAT 3 24-JUL-19 6K3A 1 JRNL REVDAT 2 10-JUL-19 6K3A 1 JRNL REVDAT 1 26-JUN-19 6K3A 0 JRNL AUTH T.JIMENJI,R.MATSUMURA,S.KORI,K.ARITA JRNL TITL STRUCTURE OF PCNA IN COMPLEX WITH DNMT1 PIP BOX REVEALS THE JRNL TITL 2 BASIS FOR THE MOLECULAR MECHANISM OF THE INTERACTION. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 516 578 2019 JRNL REFN ESSN 1090-2104 JRNL PMID 31235252 JRNL DOI 10.1016/J.BBRC.2019.06.060 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15.2_3472: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 34349 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 1783 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 40.8505 - 5.4043 0.98 2533 146 0.2069 0.2306 REMARK 3 2 5.4043 - 4.2911 0.99 2511 142 0.1627 0.2195 REMARK 3 3 4.2911 - 3.7491 0.99 2520 159 0.1814 0.2274 REMARK 3 4 3.7491 - 3.4065 0.99 2472 114 0.2099 0.1974 REMARK 3 5 3.4065 - 3.1624 0.99 2547 100 0.2385 0.3625 REMARK 3 6 3.1624 - 2.9760 0.99 2509 134 0.2589 0.3265 REMARK 3 7 2.9760 - 2.8270 1.00 2473 149 0.2797 0.3562 REMARK 3 8 2.8270 - 2.7040 1.00 2497 158 0.2732 0.3303 REMARK 3 9 2.7040 - 2.5999 1.00 2498 136 0.2721 0.3112 REMARK 3 10 2.5999 - 2.5102 1.00 2545 132 0.2790 0.3681 REMARK 3 11 2.5102 - 2.4317 1.00 2437 150 0.2867 0.3226 REMARK 3 12 2.4317 - 2.3622 1.00 2459 160 0.3010 0.3576 REMARK 3 13 2.3622 - 2.3001 1.00 2565 103 0.3192 0.4019 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.005 5694 REMARK 3 ANGLE : 0.852 7689 REMARK 3 CHIRALITY : 0.050 951 REMARK 3 PLANARITY : 0.005 948 REMARK 3 DIHEDRAL : 6.378 3462 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: NULL REMARK 4 REMARK 4 6K3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300012212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34458 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.0000 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) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.66400 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: 5MLO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M SODIUM CITRATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K 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 70.77000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.79900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.77000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.79900 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, 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 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 C 301 LIES ON A SPECIAL POSITION. 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 -2 REMARK 465 PRO A -1 REMARK 465 GLY A 0 REMARK 465 ASN A 107 REMARK 465 GLN A 108 REMARK 465 ASP A 122 REMARK 465 VAL A 123 REMARK 465 GLU A 124 REMARK 465 ALA A 163 REMARK 465 LYS A 164 REMARK 465 ASP A 165 REMARK 465 THR A 185 REMARK 465 SER A 186 REMARK 465 ASN A 187 REMARK 465 VAL A 188 REMARK 465 ASP A 189 REMARK 465 LYS A 190 REMARK 465 GLU A 191 REMARK 465 GLU A 192 REMARK 465 GLU A 258 REMARK 465 GLU A 259 REMARK 465 GLY A 260 REMARK 465 SER A 261 REMARK 465 SER B 161 REMARK 465 PRO B 175 REMARK 465 ALA B 176 REMARK 465 LYS B 177 REMARK 465 ARG B 178 REMARK 465 LYS B 179 REMARK 465 PRO B 180 REMARK 465 GLY C -2 REMARK 465 PRO C -1 REMARK 465 GLY C 0 REMARK 465 ASN C 107 REMARK 465 GLN C 108 REMARK 465 ASP C 122 REMARK 465 VAL C 123 REMARK 465 GLU C 124 REMARK 465 ALA C 163 REMARK 465 LYS C 164 REMARK 465 ASP C 165 REMARK 465 THR C 185 REMARK 465 SER C 186 REMARK 465 ASN C 187 REMARK 465 VAL C 188 REMARK 465 ASP C 189 REMARK 465 LYS C 190 REMARK 465 GLU C 191 REMARK 465 GLU C 192 REMARK 465 GLU C 258 REMARK 465 GLU C 259 REMARK 465 GLY C 260 REMARK 465 SER C 261 REMARK 465 SER D 161 REMARK 465 PRO D 175 REMARK 465 ALA D 176 REMARK 465 LYS D 177 REMARK 465 ARG D 178 REMARK 465 LYS D 179 REMARK 465 PRO D 180 REMARK 465 GLY E -2 REMARK 465 PRO E -1 REMARK 465 GLY E 0 REMARK 465 ASN E 107 REMARK 465 GLN E 108 REMARK 465 ASP E 122 REMARK 465 VAL E 123 REMARK 465 GLU E 124 REMARK 465 ALA E 163 REMARK 465 LYS E 164 REMARK 465 ASP E 165 REMARK 465 THR E 185 REMARK 465 SER E 186 REMARK 465 ASN E 187 REMARK 465 VAL E 188 REMARK 465 ASP E 189 REMARK 465 LYS E 190 REMARK 465 GLU E 191 REMARK 465 GLU E 192 REMARK 465 GLU E 258 REMARK 465 GLU E 259 REMARK 465 GLY E 260 REMARK 465 SER E 261 REMARK 465 SER F 161 REMARK 465 PRO F 175 REMARK 465 ALA F 176 REMARK 465 LYS F 177 REMARK 465 ARG F 178 REMARK 465 LYS F 179 REMARK 465 PRO F 180 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 LYS A 20 NZ REMARK 470 ARG A 53 CZ NH1 NH2 REMARK 470 ARG A 64 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 ARG A 91 CZ NH1 NH2 REMARK 470 GLU A 93 OE1 OE2 REMARK 470 ASP A 94 OD1 OD2 REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 ASP A 113 OD1 OD2 REMARK 470 GLU A 115 CD OE1 OE2 REMARK 470 LYS A 117 CD CE NZ REMARK 470 LEU A 121 CG CD1 CD2 REMARK 470 GLN A 125 OE1 NE2 REMARK 470 GLU A 132 CG CD OE1 OE2 REMARK 470 LYS A 138 NZ REMARK 470 GLU A 143 OE1 OE2 REMARK 470 CYS A 162 SG REMARK 470 LYS A 168 CE NZ REMARK 470 GLU A 174 CG CD OE1 OE2 REMARK 470 ASN A 179 OD1 ND2 REMARK 470 ILE A 180 O REMARK 470 LYS A 181 CE NZ REMARK 470 GLU A 193 CG CD OE1 OE2 REMARK 470 GLU A 198 CG CD OE1 OE2 REMARK 470 GLU A 201 CD OE1 OE2 REMARK 470 ASP A 232 OD1 OD2 REMARK 470 LYS A 240 CD CE NZ REMARK 470 ASP A 243 CG OD1 OD2 REMARK 470 GLU A 256 OE1 OE2 REMARK 470 LYS B 173 CD CE NZ REMARK 470 LYS C 13 NZ REMARK 470 ARG C 53 CZ NH1 NH2 REMARK 470 ARG C 64 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 80 CD CE NZ REMARK 470 ARG C 91 CZ NH1 NH2 REMARK 470 GLU C 93 OE1 OE2 REMARK 470 ASP C 94 CG OD1 OD2 REMARK 470 GLU C 109 CG CD OE1 OE2 REMARK 470 ASP C 113 OD1 OD2 REMARK 470 GLU C 115 CD OE1 OE2 REMARK 470 LEU C 121 CG CD1 CD2 REMARK 470 GLN C 125 CD OE1 NE2 REMARK 470 GLU C 132 CG CD OE1 OE2 REMARK 470 LYS C 138 CE NZ REMARK 470 GLU C 143 OE1 OE2 REMARK 470 CYS C 162 SG REMARK 470 LYS C 168 CE NZ REMARK 470 GLU C 174 CG CD OE1 OE2 REMARK 470 ASN C 179 OD1 ND2 REMARK 470 ILE C 180 O REMARK 470 LYS C 181 CE NZ REMARK 470 GLU C 198 CG CD OE1 OE2 REMARK 470 GLU C 201 OE1 OE2 REMARK 470 ASP C 232 OD1 OD2 REMARK 470 LYS C 240 CD CE NZ REMARK 470 ASP C 243 CG OD1 OD2 REMARK 470 LYS D 173 CD CE NZ REMARK 470 ARG E 5 CZ NH1 NH2 REMARK 470 GLN E 8 CD OE1 NE2 REMARK 470 ARG E 53 CZ NH1 NH2 REMARK 470 ARG E 61 CZ NH1 NH2 REMARK 470 ARG E 64 CG CD NE CZ NH1 NH2 REMARK 470 LYS E 80 CD CE NZ REMARK 470 ARG E 91 CZ NH1 NH2 REMARK 470 GLU E 93 OE1 OE2 REMARK 470 ASP E 94 OD1 OD2 REMARK 470 GLU E 109 CG CD OE1 OE2 REMARK 470 ASP E 113 OD1 OD2 REMARK 470 GLU E 115 CD OE1 OE2 REMARK 470 LEU E 121 CG CD1 CD2 REMARK 470 GLN E 125 CD OE1 NE2 REMARK 470 GLU E 132 CG CD OE1 OE2 REMARK 470 LYS E 138 CD CE NZ REMARK 470 GLU E 143 OE1 OE2 REMARK 470 LYS E 168 CE NZ REMARK 470 GLU E 174 CG CD OE1 OE2 REMARK 470 ASN E 179 OD1 ND2 REMARK 470 ILE E 180 O REMARK 470 LYS E 181 CE NZ REMARK 470 GLU E 193 CG CD OE1 OE2 REMARK 470 GLU E 198 CG CD OE1 OE2 REMARK 470 GLU E 201 CD OE1 OE2 REMARK 470 ASP E 232 OD1 OD2 REMARK 470 LYS E 240 CD CE NZ REMARK 470 ASP E 243 CG OD1 OD2 REMARK 470 LYS F 173 CG CD CE NZ 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 O MET A 119 O HOH A 301 2.02 REMARK 500 O SER E 42 O HOH E 301 2.12 REMARK 500 NE2 GLN C 38 O LEU C 126 2.14 REMARK 500 NE2 GLN E 38 O LEU E 126 2.15 REMARK 500 NE2 GLN A 38 O LEU A 126 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH C 312 O HOH C 312 2557 2.16 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 ILE A 87 CG1 - CB - CG2 ANGL. DEV. = -14.0 DEGREES REMARK 500 LEU E 16 CA - CB - CG ANGL. DEV. = -14.2 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 GLU A 201 144.66 -170.20 REMARK 500 ALA A 242 118.54 -38.84 REMARK 500 ASP A 243 -56.71 81.88 REMARK 500 ALA C 242 119.17 -38.69 REMARK 500 ASP C 243 -56.90 82.19 REMARK 500 LYS D 173 -67.18 -108.11 REMARK 500 GLU E 201 145.44 -171.33 REMARK 500 ALA E 242 118.61 -38.28 REMARK 500 ASP E 243 -56.17 81.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 6K3A A 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 6K3A B 161 180 UNP K7ERQ1 K7ERQ1_HUMAN 40 59 DBREF 6K3A C 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 6K3A D 161 180 UNP K7ERQ1 K7ERQ1_HUMAN 40 59 DBREF 6K3A E 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 6K3A F 161 180 UNP K7ERQ1 K7ERQ1_HUMAN 40 59 SEQADV 6K3A GLY A -2 UNP P12004 EXPRESSION TAG SEQADV 6K3A PRO A -1 UNP P12004 EXPRESSION TAG SEQADV 6K3A GLY A 0 UNP P12004 EXPRESSION TAG SEQADV 6K3A GLY C -2 UNP P12004 EXPRESSION TAG SEQADV 6K3A PRO C -1 UNP P12004 EXPRESSION TAG SEQADV 6K3A GLY C 0 UNP P12004 EXPRESSION TAG SEQADV 6K3A GLY E -2 UNP P12004 EXPRESSION TAG SEQADV 6K3A PRO E -1 UNP P12004 EXPRESSION TAG SEQADV 6K3A GLY E 0 UNP P12004 EXPRESSION TAG SEQRES 1 A 264 GLY PRO GLY MET PHE GLU ALA ARG LEU VAL GLN GLY SER SEQRES 2 A 264 ILE LEU LYS LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE SEQRES 3 A 264 ASN GLU ALA CYS TRP ASP ILE SER SER SER GLY VAL ASN SEQRES 4 A 264 LEU GLN SER MET ASP SER SER HIS VAL SER LEU VAL GLN SEQRES 5 A 264 LEU THR LEU ARG SER GLU GLY PHE ASP THR TYR ARG CYS SEQRES 6 A 264 ASP ARG ASN LEU ALA MET GLY VAL ASN LEU THR SER MET SEQRES 7 A 264 SER LYS ILE LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE SEQRES 8 A 264 THR LEU ARG ALA GLU ASP ASN ALA ASP THR LEU ALA LEU SEQRES 9 A 264 VAL PHE GLU ALA PRO ASN GLN GLU LYS VAL SER ASP TYR SEQRES 10 A 264 GLU MET LYS LEU MET ASP LEU ASP VAL GLU GLN LEU GLY SEQRES 11 A 264 ILE PRO GLU GLN GLU TYR SER CYS VAL VAL LYS MET PRO SEQRES 12 A 264 SER GLY GLU PHE ALA ARG ILE CYS ARG ASP LEU SER HIS SEQRES 13 A 264 ILE GLY ASP ALA VAL VAL ILE SER CYS ALA LYS ASP GLY SEQRES 14 A 264 VAL LYS PHE SER ALA SER GLY GLU LEU GLY ASN GLY ASN SEQRES 15 A 264 ILE LYS LEU SER GLN THR SER ASN VAL ASP LYS GLU GLU SEQRES 16 A 264 GLU ALA VAL THR ILE GLU MET ASN GLU PRO VAL GLN LEU SEQRES 17 A 264 THR PHE ALA LEU ARG TYR LEU ASN PHE PHE THR LYS ALA SEQRES 18 A 264 THR PRO LEU SER SER THR VAL THR LEU SER MET SER ALA SEQRES 19 A 264 ASP VAL PRO LEU VAL VAL GLU TYR LYS ILE ALA ASP MET SEQRES 20 A 264 GLY HIS LEU LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP SEQRES 21 A 264 GLU GLU GLY SER SEQRES 1 B 20 SER THR ARG GLN THR THR ILE THR SER HIS PHE ALA LYS SEQRES 2 B 20 GLY PRO ALA LYS ARG LYS PRO SEQRES 1 C 264 GLY PRO GLY MET PHE GLU ALA ARG LEU VAL GLN GLY SER SEQRES 2 C 264 ILE LEU LYS LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE SEQRES 3 C 264 ASN GLU ALA CYS TRP ASP ILE SER SER SER GLY VAL ASN SEQRES 4 C 264 LEU GLN SER MET ASP SER SER HIS VAL SER LEU VAL GLN SEQRES 5 C 264 LEU THR LEU ARG SER GLU GLY PHE ASP THR TYR ARG CYS SEQRES 6 C 264 ASP ARG ASN LEU ALA MET GLY VAL ASN LEU THR SER MET SEQRES 7 C 264 SER LYS ILE LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE SEQRES 8 C 264 THR LEU ARG ALA GLU ASP ASN ALA ASP THR LEU ALA LEU SEQRES 9 C 264 VAL PHE GLU ALA PRO ASN GLN GLU LYS VAL SER ASP TYR SEQRES 10 C 264 GLU MET LYS LEU MET ASP LEU ASP VAL GLU GLN LEU GLY SEQRES 11 C 264 ILE PRO GLU GLN GLU TYR SER CYS VAL VAL LYS MET PRO SEQRES 12 C 264 SER GLY GLU PHE ALA ARG ILE CYS ARG ASP LEU SER HIS SEQRES 13 C 264 ILE GLY ASP ALA VAL VAL ILE SER CYS ALA LYS ASP GLY SEQRES 14 C 264 VAL LYS PHE SER ALA SER GLY GLU LEU GLY ASN GLY ASN SEQRES 15 C 264 ILE LYS LEU SER GLN THR SER ASN VAL ASP LYS GLU GLU SEQRES 16 C 264 GLU ALA VAL THR ILE GLU MET ASN GLU PRO VAL GLN LEU SEQRES 17 C 264 THR PHE ALA LEU ARG TYR LEU ASN PHE PHE THR LYS ALA SEQRES 18 C 264 THR PRO LEU SER SER THR VAL THR LEU SER MET SER ALA SEQRES 19 C 264 ASP VAL PRO LEU VAL VAL GLU TYR LYS ILE ALA ASP MET SEQRES 20 C 264 GLY HIS LEU LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP SEQRES 21 C 264 GLU GLU GLY SER SEQRES 1 D 20 SER THR ARG GLN THR THR ILE THR SER HIS PHE ALA LYS SEQRES 2 D 20 GLY PRO ALA LYS ARG LYS PRO SEQRES 1 E 264 GLY PRO GLY MET PHE GLU ALA ARG LEU VAL GLN GLY SER SEQRES 2 E 264 ILE LEU LYS LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE SEQRES 3 E 264 ASN GLU ALA CYS TRP ASP ILE SER SER SER GLY VAL ASN SEQRES 4 E 264 LEU GLN SER MET ASP SER SER HIS VAL SER LEU VAL GLN SEQRES 5 E 264 LEU THR LEU ARG SER GLU GLY PHE ASP THR TYR ARG CYS SEQRES 6 E 264 ASP ARG ASN LEU ALA MET GLY VAL ASN LEU THR SER MET SEQRES 7 E 264 SER LYS ILE LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE SEQRES 8 E 264 THR LEU ARG ALA GLU ASP ASN ALA ASP THR LEU ALA LEU SEQRES 9 E 264 VAL PHE GLU ALA PRO ASN GLN GLU LYS VAL SER ASP TYR SEQRES 10 E 264 GLU MET LYS LEU MET ASP LEU ASP VAL GLU GLN LEU GLY SEQRES 11 E 264 ILE PRO GLU GLN GLU TYR SER CYS VAL VAL LYS MET PRO SEQRES 12 E 264 SER GLY GLU PHE ALA ARG ILE CYS ARG ASP LEU SER HIS SEQRES 13 E 264 ILE GLY ASP ALA VAL VAL ILE SER CYS ALA LYS ASP GLY SEQRES 14 E 264 VAL LYS PHE SER ALA SER GLY GLU LEU GLY ASN GLY ASN SEQRES 15 E 264 ILE LYS LEU SER GLN THR SER ASN VAL ASP LYS GLU GLU SEQRES 16 E 264 GLU ALA VAL THR ILE GLU MET ASN GLU PRO VAL GLN LEU SEQRES 17 E 264 THR PHE ALA LEU ARG TYR LEU ASN PHE PHE THR LYS ALA SEQRES 18 E 264 THR PRO LEU SER SER THR VAL THR LEU SER MET SER ALA SEQRES 19 E 264 ASP VAL PRO LEU VAL VAL GLU TYR LYS ILE ALA ASP MET SEQRES 20 E 264 GLY HIS LEU LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP SEQRES 21 E 264 GLU GLU GLY SER SEQRES 1 F 20 SER THR ARG GLN THR THR ILE THR SER HIS PHE ALA LYS SEQRES 2 F 20 GLY PRO ALA LYS ARG LYS PRO FORMUL 7 HOH *46(H2 O) HELIX 1 AA1 GLY A 9 LYS A 20 1 12 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 HIS A 153 1 13 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 THR B 166 HIS B 170 5 5 HELIX 8 AA8 GLY C 9 LYS C 20 1 12 HELIX 9 AA9 GLU C 55 PHE C 57 5 3 HELIX 10 AB1 LEU C 72 LYS C 80 1 9 HELIX 11 AB2 SER C 141 HIS C 153 1 13 HELIX 12 AB3 LEU C 209 THR C 216 1 8 HELIX 13 AB4 LYS C 217 SER C 222 5 6 HELIX 14 AB5 THR D 166 HIS D 170 5 5 HELIX 15 AB6 GLY E 9 LYS E 20 1 12 HELIX 16 AB7 GLU E 55 PHE E 57 5 3 HELIX 17 AB8 LEU E 72 LYS E 80 1 9 HELIX 18 AB9 SER E 141 HIS E 153 1 13 HELIX 19 AC1 LEU E 209 THR E 216 1 8 HELIX 20 AC2 LYS E 217 SER E 222 5 6 HELIX 21 AC3 THR F 166 HIS F 170 5 5 SHEET 1 AA1 9 THR A 59 CYS A 62 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 ALA A 100 N ARG A 91 SHEET 5 AA1 9 VAL A 111 LYS A 117 -1 O TYR A 114 N LEU A 101 SHEET 6 AA1 9 GLY E 176 ASN E 179 -1 O ASN E 179 N ASP A 113 SHEET 7 AA1 9 LYS E 168 SER E 172 -1 N ALA E 171 O GLY E 178 SHEET 8 AA1 9 ALA E 157 CYS E 162 -1 N SER E 161 O LYS E 168 SHEET 9 AA1 9 VAL E 203 ALA E 208 -1 O LEU E 205 N ILE E 160 SHEET 1 AA2 9 LEU A 66 ASN A 71 0 SHEET 2 AA2 9 GLU A 25 SER A 31 -1 N ILE A 30 O LEU A 66 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 LYS A 248 N GLN A 49 SHEET 6 AA2 9 LEU A 235 ILE A 241 -1 N TYR A 239 O LEU A 247 SHEET 7 AA2 9 THR A 224 MET A 229 -1 N SER A 228 O VAL A 236 SHEET 8 AA2 9 CYS A 135 PRO A 140 -1 N MET A 139 O VAL A 225 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 LYS A 168 SER A 172 -1 O LYS A 168 N SER A 161 SHEET 4 AA3 9 GLY A 176 ASN A 179 -1 O GLY A 178 N ALA A 171 SHEET 5 AA3 9 VAL C 111 LYS C 117 -1 O ASP C 113 N ASN A 179 SHEET 6 AA3 9 THR C 98 GLU C 104 -1 N LEU C 101 O TYR C 114 SHEET 7 AA3 9 ILE C 87 ALA C 92 -1 N ILE C 87 O GLU C 104 SHEET 8 AA3 9 PHE C 2 LEU C 6 -1 N LEU C 6 O ILE C 88 SHEET 9 AA3 9 THR C 59 CYS C 62 -1 O THR C 59 N ARG C 5 SHEET 1 AA4 2 LYS A 254 ILE A 255 0 SHEET 2 AA4 2 ARG B 163 GLN B 164 -1 O ARG B 163 N ILE A 255 SHEET 1 AA5 9 LEU C 66 ASN C 71 0 SHEET 2 AA5 9 GLU C 25 SER C 31 -1 N ILE C 30 O LEU C 66 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 LYS C 248 N GLN C 49 SHEET 6 AA5 9 LEU C 235 ILE C 241 -1 N TYR C 239 O LEU C 247 SHEET 7 AA5 9 THR C 224 MET C 229 -1 N SER C 228 O VAL C 236 SHEET 8 AA5 9 CYS C 135 PRO C 140 -1 N CYS C 135 O MET C 229 SHEET 9 AA5 9 THR C 196 MET C 199 -1 O THR C 196 N LYS C 138 SHEET 1 AA6 9 VAL C 203 ALA C 208 0 SHEET 2 AA6 9 ALA C 157 CYS C 162 -1 N ILE C 160 O LEU C 205 SHEET 3 AA6 9 LYS C 168 GLY C 173 -1 O LYS C 168 N SER C 161 SHEET 4 AA6 9 GLY C 176 ASN C 179 -1 O GLY C 176 N GLY C 173 SHEET 5 AA6 9 VAL E 111 LYS E 117 -1 O ASP E 113 N ASN C 179 SHEET 6 AA6 9 THR E 98 GLU E 104 -1 N LEU E 101 O TYR E 114 SHEET 7 AA6 9 ILE E 87 ALA E 92 -1 N ARG E 91 O ALA E 100 SHEET 8 AA6 9 PHE E 2 LEU E 6 -1 N PHE E 2 O ALA E 92 SHEET 9 AA6 9 THR E 59 CYS E 62 -1 O THR E 59 N ARG E 5 SHEET 1 AA7 2 LYS C 254 ILE C 255 0 SHEET 2 AA7 2 ARG D 163 GLN D 164 -1 O ARG D 163 N ILE C 255 SHEET 1 AA8 9 LEU E 66 ASN E 71 0 SHEET 2 AA8 9 GLU E 25 SER E 31 -1 N ILE E 30 O LEU E 66 SHEET 3 AA8 9 GLY E 34 MET E 40 -1 O ASN E 36 N ASP E 29 SHEET 4 AA8 9 SER E 46 ARG E 53 -1 O LEU E 50 N LEU E 37 SHEET 5 AA8 9 GLY E 245 LEU E 251 -1 O LYS E 248 N GLN E 49 SHEET 6 AA8 9 LEU E 235 ILE E 241 -1 N VAL E 237 O TYR E 249 SHEET 7 AA8 9 THR E 224 MET E 229 -1 N SER E 228 O VAL E 236 SHEET 8 AA8 9 CYS E 135 PRO E 140 -1 N CYS E 135 O MET E 229 SHEET 9 AA8 9 THR E 196 MET E 199 -1 O THR E 196 N LYS E 138 SHEET 1 AA9 2 LYS E 254 ILE E 255 0 SHEET 2 AA9 2 ARG F 163 GLN F 164 -1 O ARG F 163 N ILE E 255 CRYST1 141.540 81.598 68.105 90.00 90.02 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 0.007065 0.000000 0.000003 0.00000 SCALE2 0.000000 0.012255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014683 0.00000