PDB Short entry for 3V61 HEADER PROTEIN BINDING/DNA BINDING PROTEIN 18-DEC-11 3V61 TITLE STRUCTURE OF S. CEREVISIAE PCNA CONJUGATED TO SUMO ON LYSINE 164 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE PROTEIN SMT3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 20-98; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROLIFERATING CELL NUCLEAR ANTIGEN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: PCNA; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: W3031A; SOURCE 6 GENE: D9719.15, SMT3, YDR510W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 14 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 15 ORGANISM_TAXID: 559292; SOURCE 16 STRAIN: W3031A; SOURCE 17 GENE: POL30, YBR0811, YBR088C; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CP RIL; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS UBIQUITIN-LIKE PROTEIN PCNA, POST-TRANSLATIONAL MODIFICATION, DNA KEYWDS 2 REPLICATION, DNA DAMAGE RESPONSE, SRS2, NEM MODIFICATION ON PCNA KEYWDS 3 CYS22 AND CYS81, NUCLEAR, PROTEIN BINDING-DNA BINDING PROTEIN KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.A.ARMSTRONG,F.MOHIDEEN,C.D.LIMA REVDAT 6 13-SEP-23 3V61 1 REMARK SEQADV LINK REVDAT 5 25-OCT-17 3V61 1 REMARK REVDAT 4 18-SEP-13 3V61 1 REMARK REVDAT 3 03-APR-13 3V61 1 JRNL REVDAT 2 07-MAR-12 3V61 1 JRNL REVDAT 1 29-FEB-12 3V61 0 JRNL AUTH A.A.ARMSTRONG,F.MOHIDEEN,C.D.LIMA JRNL TITL RECOGNITION OF SUMO-MODIFIED PCNA REQUIRES TANDEM RECEPTOR JRNL TITL 2 MOTIFS IN SRS2. JRNL REF NATURE V. 483 59 2012 JRNL REFN ISSN 0028-0836 JRNL PMID 22382979 JRNL DOI 10.1038/NATURE10883 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12550 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 617 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 842 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2604 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.14000 REMARK 3 B22 (A**2) : -2.14000 REMARK 3 B33 (A**2) : 4.27000 REMARK 3 B12 (A**2) : 0.00000 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): 0.997 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.347 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.187 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.592 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2663 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3581 ; 1.289 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 5.807 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;36.634 ;25.250 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 505 ;19.093 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.472 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 413 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1978 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1647 ; 0.608 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2663 ; 1.147 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1016 ; 1.251 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 918 ; 2.178 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 NEM MOLECULE HAS OCCUPANCY OF 1 AS MASS SPEC SUGGESTED THAT THIS REMARK 3 LIGAND IS REMARK 3 FULLY MODIFIED IN THE STUDIED SAMPLES. REMARK 4 REMARK 4 3V61 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069639. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-06 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23649 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.37600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRIES 1PLQ AND 1EUV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% MPD, 100 MM BACL2, 100 MM BIS REMARK 280 -TRIS, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 70.03000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 70.03000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.05950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 70.03000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.02975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 70.03000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.08925 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 70.03000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.03000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.05950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 70.03000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 39.08925 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 70.03000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 13.02975 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: PCNA IS NORMALLY A TRIMER BUT NEM MODIFICATION DISRUPTS THE REMARK 300 TRIMER AND CAUSES PCNA TO RUN AS A MONOMER ON GEL FILTRATION THIS REMARK 300 SUMO-PCNA MONOMER CRYSTALLIZES BY REFORMING THE PCNA:PCNA PROTOMER REMARK 300 BUT WITH A RIGHT HANDED HELICAL SCREW COINCIDENT WITH THE I41 SCREW REMARK 300 AXIS THE UNIT CELL CONTAINS ONE TURN OF THIS HELICAL SCREW 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 400 REMARK 400 COMPOUND REMARK 400 THERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUES A98 AND B164 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 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 REMARK 465 MET A 18 REMARK 465 ARG A 19 REMARK 465 PRO A 20 REMARK 465 GLU A 21 REMARK 465 ASN B 255 REMARK 465 ASP B 256 REMARK 465 GLU B 257 REMARK 465 GLU B 258 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 84 CG CD OE1 OE2 REMARK 470 PHE B 254 CG CD1 CD2 CE1 CE2 CZ 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 GLY A 98 NZ LYS B 164 1.92 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 ASP A 30 -127.74 -102.50 REMARK 500 LYS B 107 -13.60 83.92 REMARK 500 LYS B 108 37.93 91.58 REMARK 500 ASP B 109 -79.75 -79.43 REMARK 500 ALA B 123 132.89 -39.97 REMARK 500 LEU B 126 43.24 -106.98 REMARK 500 GLU B 130 112.05 42.85 REMARK 500 GLU B 165 19.24 52.12 REMARK 500 PHE B 185 117.96 -164.12 REMARK 500 GLN B 201 135.87 -177.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA A 2 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 82 OD2 REMARK 620 2 ASP A 82 O 50.0 REMARK 620 3 HOH A 100 O 86.0 64.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA A 3 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 6 O REMARK 620 2 ASP A 87 OD1 125.8 REMARK 620 3 HOH A 104 O 92.7 134.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA A 11 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 113 O REMARK 620 2 HOH B 277 O 49.7 REMARK 620 3 HOH B 293 O 95.7 46.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 265 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 108 O REMARK 620 2 HOH B 271 O 134.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 263 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 7 O REMARK 620 2 THR B 85 O 94.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 259 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 21 O REMARK 620 2 ASP B 214 OD1 99.4 REMARK 620 3 HOH B 280 O 89.2 91.5 REMARK 620 4 HOH B 323 O 73.8 145.1 54.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 262 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 55 O REMARK 620 2 HOH B 279 O 111.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 261 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 57 O REMARK 620 2 HOH B 294 O 129.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 267 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 80 O REMARK 620 2 GLY B 82 O 62.4 REMARK 620 3 HOH B 274 O 76.0 74.4 REMARK 620 4 HOH B 276 O 147.0 86.5 85.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 264 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 93 OD1 REMARK 620 2 THR B 95 OG1 88.6 REMARK 620 3 THR B 95 O 100.0 49.4 REMARK 620 4 HOH B 340 O 158.2 84.1 60.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 260 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 240 OD2 REMARK 620 2 LEU B 241 O 75.8 REMARK 620 3 HOH B 270 O 102.2 67.2 REMARK 620 4 HOH B 322 O 105.1 51.2 100.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NEQ B 268 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NEQ B 269 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3V60 RELATED DB: PDB REMARK 900 RELATED ID: 3V62 RELATED DB: PDB DBREF 3V61 A 20 98 UNP Q12306 SMT3_YEAST 20 98 DBREF 3V61 B 1 258 UNP P15873 PCNA_YEAST 1 258 SEQADV 3V61 GLY A 15 UNP Q12306 EXPRESSION TAG SEQADV 3V61 SER A 16 UNP Q12306 EXPRESSION TAG SEQADV 3V61 HIS A 17 UNP Q12306 EXPRESSION TAG SEQADV 3V61 MET A 18 UNP Q12306 EXPRESSION TAG SEQADV 3V61 ARG A 19 UNP Q12306 EXPRESSION TAG SEQADV 3V61 GLY B 127 UNP P15873 LYS 127 ENGINEERED MUTATION SEQRES 1 A 84 GLY SER HIS MET ARG PRO GLU THR HIS ILE ASN LEU LYS SEQRES 2 A 84 VAL SER ASP GLY SER SER GLU ILE PHE PHE LYS ILE LYS SEQRES 3 A 84 LYS THR THR PRO LEU ARG ARG LEU MET GLU ALA PHE ALA SEQRES 4 A 84 LYS ARG GLN GLY LYS GLU MET ASP SER LEU ARG PHE LEU SEQRES 5 A 84 TYR ASP GLY ILE ARG ILE GLN ALA ASP GLN THR PRO GLU SEQRES 6 A 84 ASP LEU ASP MET GLU ASP ASN ASP ILE ILE GLU ALA HIS SEQRES 7 A 84 ARG GLU GLN ILE GLY GLY SEQRES 1 B 258 MET LEU GLU ALA LYS PHE GLU GLU ALA SER LEU PHE LYS SEQRES 2 B 258 ARG ILE ILE ASP GLY PHE LYS ASP CYS VAL GLN LEU VAL SEQRES 3 B 258 ASN PHE GLN CYS LYS GLU ASP GLY ILE ILE ALA GLN ALA SEQRES 4 B 258 VAL ASP ASP SER ARG VAL LEU LEU VAL SER LEU GLU ILE SEQRES 5 B 258 GLY VAL GLU ALA PHE GLN GLU TYR ARG CYS ASP HIS PRO SEQRES 6 B 258 VAL THR LEU GLY MET ASP LEU THR SER LEU SER LYS ILE SEQRES 7 B 258 LEU ARG CYS GLY ASN ASN THR ASP THR LEU THR LEU ILE SEQRES 8 B 258 ALA ASP ASN THR PRO ASP SER ILE ILE LEU LEU PHE GLU SEQRES 9 B 258 ASP THR LYS LYS ASP ARG ILE ALA GLU TYR SER LEU LYS SEQRES 10 B 258 LEU MET ASP ILE ASP ALA ASP PHE LEU GLY ILE GLU GLU SEQRES 11 B 258 LEU GLN TYR ASP SER THR LEU SER LEU PRO SER SER GLU SEQRES 12 B 258 PHE SER LYS ILE VAL ARG ASP LEU SER GLN LEU SER ASP SEQRES 13 B 258 SER ILE ASN ILE MET ILE THR LYS GLU THR ILE LYS PHE SEQRES 14 B 258 VAL ALA ASP GLY ASP ILE GLY SER GLY SER VAL ILE ILE SEQRES 15 B 258 LYS PRO PHE VAL ASP MET GLU HIS PRO GLU THR SER ILE SEQRES 16 B 258 LYS LEU GLU MET ASP GLN PRO VAL ASP LEU THR PHE GLY SEQRES 17 B 258 ALA LYS TYR LEU LEU ASP ILE ILE LYS GLY SER SER LEU SEQRES 18 B 258 SER ASP ARG VAL GLY ILE ARG LEU SER SER GLU ALA PRO SEQRES 19 B 258 ALA LEU PHE GLN PHE ASP LEU LYS SER GLY PHE LEU GLN SEQRES 20 B 258 PHE PHE LEU ALA PRO LYS PHE ASN ASP GLU GLU HET BA A 2 1 HET BA A 3 1 HET BA A 4 1 HET BA A 11 1 HET BA B 259 1 HET BA B 260 1 HET BA B 261 1 HET BA B 262 1 HET BA B 263 1 HET BA B 264 1 HET BA B 265 1 HET BA B 266 1 HET BA B 267 1 HET NEQ B 268 9 HET NEQ B 269 9 HETNAM BA BARIUM ION HETNAM NEQ N-ETHYLMALEIMIDE FORMUL 3 BA 13(BA 2+) FORMUL 16 NEQ 2(C6 H7 N O2) FORMUL 18 HOH *90(H2 O) HELIX 1 1 LEU A 45 ARG A 55 1 11 HELIX 2 2 GLU A 59 ASP A 61 5 3 HELIX 3 3 THR A 77 ASP A 82 1 6 HELIX 4 4 GLU B 8 VAL B 23 1 16 HELIX 5 5 GLU B 55 PHE B 57 5 3 HELIX 6 6 LEU B 72 GLY B 82 1 11 HELIX 7 7 THR B 106 ASP B 109 5 4 HELIX 8 8 SER B 141 GLN B 153 1 13 HELIX 9 9 HIS B 190 SER B 194 5 5 HELIX 10 10 ALA B 209 LYS B 217 1 9 HELIX 11 11 GLY B 218 LEU B 221 5 4 SHEET 1 A 5 GLU A 34 LYS A 38 0 SHEET 2 A 5 ASN A 25 SER A 29 -1 N VAL A 28 O ILE A 35 SHEET 3 A 5 ILE A 88 ARG A 93 1 O ALA A 91 N SER A 29 SHEET 4 A 5 LEU A 63 TYR A 67 -1 N ARG A 64 O HIS A 92 SHEET 5 A 5 ILE A 70 ARG A 71 -1 O ILE A 70 N TYR A 67 SHEET 1 B 5 GLU B 59 CYS B 62 0 SHEET 2 B 5 LEU B 2 PHE B 6 -1 N GLU B 3 O ARG B 61 SHEET 3 B 5 THR B 87 ALA B 92 -1 O ALA B 92 N LEU B 2 SHEET 4 B 5 SER B 98 GLU B 104 -1 O ILE B 100 N ILE B 91 SHEET 5 B 5 ILE B 111 LYS B 117 -1 O ALA B 112 N PHE B 103 SHEET 1 C 9 VAL B 66 ASP B 71 0 SHEET 2 C 9 LEU B 25 LYS B 31 -1 N CYS B 30 O VAL B 66 SHEET 3 C 9 GLY B 34 VAL B 40 -1 O GLY B 34 N LYS B 31 SHEET 4 C 9 LEU B 46 GLY B 53 -1 O LEU B 50 N ALA B 37 SHEET 5 C 9 GLY B 244 LEU B 250 -1 O PHE B 245 N GLU B 51 SHEET 6 C 9 ALA B 235 ASP B 240 -1 N ALA B 235 O LEU B 250 SHEET 7 C 9 ARG B 224 LEU B 229 -1 N GLY B 226 O GLN B 238 SHEET 8 C 9 SER B 135 PRO B 140 -1 N LEU B 137 O ILE B 227 SHEET 9 C 9 LYS B 196 MET B 199 -1 O LYS B 196 N SER B 138 SHEET 1 D 4 SER B 177 ILE B 182 0 SHEET 2 D 4 THR B 166 ASP B 172 -1 N ALA B 171 O GLY B 178 SHEET 3 D 4 SER B 157 THR B 163 -1 N ASN B 159 O VAL B 170 SHEET 4 D 4 VAL B 203 GLY B 208 -1 O PHE B 207 N ILE B 158 LINK C GLY A 98 NZ LYS B 164 1555 1555 1.35 LINK SG CYS B 22 C3 NEQ B 268 1555 1555 1.69 LINK SG CYS B 81 C3 NEQ B 269 1555 1555 1.66 LINK BA BA A 2 OD2 ASP A 82 1555 1555 2.62 LINK BA BA A 2 O ASP A 82 1555 1555 3.20 LINK BA BA A 2 O HOH A 100 1555 1555 2.61 LINK BA BA A 3 O HOH A 6 1555 1555 3.34 LINK BA BA A 3 OD1 ASP A 87 1555 1555 2.89 LINK BA BA A 3 O HOH A 104 1555 1555 3.36 LINK BA BA A 4 OD2 ASP A 82 1555 1555 3.11 LINK BA BA A 11 O HOH A 113 1555 1555 2.99 LINK BA BA A 11 O HOH B 277 1555 1555 3.40 LINK BA BA A 11 O HOH B 293 1555 1555 3.29 LINK O HOH A 108 BA BA B 265 1555 1555 2.87 LINK O GLU B 7 BA BA B 263 1555 1555 3.14 LINK O ASP B 21 BA BA B 259 1555 1555 3.13 LINK O GLU B 55 BA BA B 262 1555 1555 3.08 LINK O PHE B 57 BA BA B 261 1555 1555 2.98 LINK O ARG B 80 BA BA B 267 1555 1555 2.98 LINK O GLY B 82 BA BA B 267 1555 1555 3.30 LINK O THR B 85 BA BA B 263 1555 1555 3.10 LINK OD1 ASP B 93 BA BA B 264 1555 1555 2.89 LINK OG1 THR B 95 BA BA B 264 1555 1555 3.15 LINK O THR B 95 BA BA B 264 1555 1555 3.23 LINK OD1 ASP B 214 BA BA B 259 1555 1555 3.06 LINK OD2 ASP B 240 BA BA B 260 1555 1555 3.01 LINK O LEU B 241 BA BA B 260 1555 1555 2.83 LINK BA BA B 259 O HOH B 280 1555 1555 2.96 LINK BA BA B 259 O HOH B 323 1555 1555 2.86 LINK BA BA B 260 O HOH B 270 1555 1555 2.91 LINK BA BA B 260 O HOH B 322 1555 1555 2.92 LINK BA BA B 261 O HOH B 294 1555 1555 3.32 LINK BA BA B 262 O HOH B 279 1555 1555 3.35 LINK BA BA B 264 O HOH B 340 1555 1555 2.55 LINK BA BA B 265 O HOH B 271 1555 1555 3.34 LINK BA BA B 267 O HOH B 274 1555 1555 2.82 LINK BA BA B 267 O HOH B 276 1555 1555 3.00 CISPEP 1 GLY A 97 GLY A 98 0 -3.98 SITE 1 AC1 4 HOH A 6 ASP A 82 ASP A 85 HOH A 100 SITE 1 AC2 1 ASP A 87 SITE 1 AC3 3 HIS A 23 ASP A 82 ASP A 85 SITE 1 AC4 2 HOH A 113 ASP B 33 SITE 1 AC5 5 ASP B 21 ASP B 214 HOH B 275 HOH B 280 SITE 2 AC5 5 HOH B 323 SITE 1 AC6 5 ASP B 240 LEU B 241 HOH B 270 HOH B 273 SITE 2 AC6 5 HOH B 322 SITE 1 AC7 3 PHE B 57 BA B 262 HOH B 299 SITE 1 AC8 2 GLU B 55 BA B 261 SITE 1 AC9 3 GLU B 7 THR B 85 THR B 87 SITE 1 BC1 4 ASP B 93 ASN B 94 THR B 95 HOH B 340 SITE 1 BC2 2 HOH A 108 HOH B 293 SITE 1 BC3 1 ASP B 172 SITE 1 BC4 4 ARG B 80 GLY B 82 HOH B 274 HOH B 276 SITE 1 BC5 5 GLY B 18 PHE B 19 CYS B 22 VAL B 48 SITE 2 BC5 5 ASP B 214 SITE 1 BC6 6 ILE B 78 CYS B 81 ASP B 150 GLN B 153 SITE 2 BC6 6 LEU B 154 HOH B 324 CRYST1 140.060 140.060 52.119 90.00 90.00 90.00 I 41 8 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 0.007140 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019187 0.00000