HEADER DNA BINDING PROTEIN 24-FEB-10 3LX2 TITLE CRYSTAL STRUCTURE ANALYSIS OF PCNA FROM THERMOCOCCUS KODAKARAENSIS TITLE 2 TK0582 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE SLIDING CLAMP 2; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG 2, PCNA 2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_COMMON: THERMOCOCCUS KODAKARAENSIS; SOURCE 4 ORGANISM_TAXID: 311400; SOURCE 5 GENE: PCN2, TK0535, TK0582; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA KEYWDS PCNA, DNA PROCESSIVITY FACTOR, TRIMER, TOROIDAL, DNA REPLICATION, KEYWDS 2 DNA-BINDING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.E.LADNER,Z.KELMAN,M.PAN REVDAT 2 20-JUN-12 3LX2 1 JRNL VERSN REVDAT 1 26-JAN-11 3LX2 0 JRNL AUTH J.E.LADNER,M.PAN,J.HURWITZ,Z.KELMAN JRNL TITL CRYSTAL STRUCTURES OF TWO ACTIVE PROLIFERATING CELL NUCLEAR JRNL TITL 2 ANTIGENS (PCNAS) ENCODED BY THERMOCOCCUS KODAKARAENSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 2711 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21270332 JRNL DOI 10.1073/PNAS.1019179108 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 35927 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) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1798 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4744 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 253 REMARK 3 BIN FREE R VALUE : 0.4900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5851 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.69000 REMARK 3 B22 (A**2) : -2.28000 REMARK 3 B33 (A**2) : 0.60000 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): 0.468 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.323 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.266 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.389 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5980 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8089 ; 1.796 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 736 ; 7.168 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 255 ;37.905 ;24.118 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1096 ;19.450 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;22.152 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 944 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4369 ; 0.008 ; 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): 3689 ; 0.965 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5964 ; 1.803 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2291 ; 2.559 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2125 ; 4.295 ; 4.500 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 3LX2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB057837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2-5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36454 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 2.830 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.72 REMARK 200 R MERGE FOR SHELL (I) : 0.34500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4-2.8 M AMMONIUM SULFATE, 100 MM REMARK 280 SODIUM CITRATE, 5-10% 2,4-METHYL PENTANEDIOL. THE PROTEIN REMARK 280 SOLUTION HAS 10% GLYCEROL, VAPOR DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 61.98500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.98500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 60.24000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.13500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.24000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.13500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 61.98500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.24000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.13500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.98500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.24000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.13500 REMARK 290 SMTRY3 8 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL 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 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 MET A 1 REMARK 465 GLU A 249 REMARK 465 GLU A 250 REMARK 465 GLY A 251 REMARK 465 ARG A 252 REMARK 465 SER A 253 REMARK 465 HIS A 254 REMARK 465 HIS A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 MET B 1 REMARK 465 VAL B 248 REMARK 465 GLU B 249 REMARK 465 GLU B 250 REMARK 465 GLY B 251 REMARK 465 ARG B 252 REMARK 465 SER B 253 REMARK 465 HIS B 254 REMARK 465 HIS B 255 REMARK 465 HIS B 256 REMARK 465 HIS B 257 REMARK 465 HIS B 258 REMARK 465 HIS B 259 REMARK 465 MET C 1 REMARK 465 VAL C 248 REMARK 465 GLU C 249 REMARK 465 GLU C 250 REMARK 465 GLY C 251 REMARK 465 ARG C 252 REMARK 465 SER C 253 REMARK 465 HIS C 254 REMARK 465 HIS C 255 REMARK 465 HIS C 256 REMARK 465 HIS C 257 REMARK 465 HIS C 258 REMARK 465 HIS C 259 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 SER B 85 O4 SO4 B 261 2.10 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 11 NE - CZ - NH1 ANGL. DEV. = 3.2 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 64 -96.34 -93.76 REMARK 500 GLU A 96 -176.42 -66.06 REMARK 500 ASN A 97 57.11 -106.81 REMARK 500 PRO A 129 70.97 -68.05 REMARK 500 LYS A 192 55.40 -93.82 REMARK 500 MET A 193 -139.79 156.42 REMARK 500 THR A 194 -26.12 -151.73 REMARK 500 ALA A 237 -58.50 169.43 REMARK 500 PRO A 246 -171.93 -69.56 REMARK 500 ARG B 45 38.92 72.59 REMARK 500 MET B 56 -36.52 -29.33 REMARK 500 ASN B 171 -89.63 55.48 REMARK 500 ASP B 172 53.23 -151.92 REMARK 500 ARG B 235 42.71 26.69 REMARK 500 ASP B 236 -47.40 80.78 REMARK 500 PHE C 23 -31.16 -131.08 REMARK 500 ALA C 40 136.81 -179.11 REMARK 500 PRO C 43 -46.10 -27.85 REMARK 500 TYR C 61 44.08 -148.86 REMARK 500 VAL C 63 81.15 -153.97 REMARK 500 ASN C 97 51.80 -90.96 REMARK 500 ALA C 118 39.66 -77.85 REMARK 500 PRO C 129 48.55 -76.57 REMARK 500 ASP C 172 17.32 162.21 REMARK 500 LYS C 197 113.48 -170.09 REMARK 500 ASP C 225 57.32 36.19 REMARK 500 ARG C 235 41.84 35.80 REMARK 500 ALA C 237 -60.87 -156.73 REMARK 500 PRO C 246 -168.12 -100.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN B 119 24.7 L L OUTSIDE RANGE REMARK 500 LYS B 167 24.5 L L OUTSIDE RANGE REMARK 500 ASP B 225 24.5 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 270 DISTANCE = 5.20 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 260 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LX1 RELATED DB: PDB DBREF 3LX2 A 1 253 UNP Q5JFD3 PCNA2_PYRKO 1 253 DBREF 3LX2 B 1 253 UNP Q5JFD3 PCNA2_PYRKO 1 253 DBREF 3LX2 C 1 253 UNP Q5JFD3 PCNA2_PYRKO 1 253 SEQADV 3LX2 HIS A 254 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS A 255 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS A 256 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS A 257 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS A 258 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS A 259 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS B 254 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS B 255 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS B 256 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS B 257 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS B 258 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS B 259 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS C 254 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS C 255 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS C 256 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS C 257 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS C 258 UNP Q5JFD3 EXPRESSION TAG SEQADV 3LX2 HIS C 259 UNP Q5JFD3 EXPRESSION TAG SEQRES 1 A 259 MET THR PHE GLU ILE VAL PHE ASP SER ALA ARG GLU PHE SEQRES 2 A 259 GLU SER LEU ILE ALA THR LEU GLU LYS PHE PHE ASP GLU SEQRES 3 A 259 ALA VAL PHE GLN VAL ASN MET GLU GLY ILE GLN MET ARG SEQRES 4 A 259 ALA ILE ASP PRO SER ARG VAL VAL LEU VAL ASP LEU ASN SEQRES 5 A 259 LEU PRO GLU MET LEU PHE SER LYS TYR SER VAL GLU SER SEQRES 6 A 259 GLU GLU ALA ILE ALA PHE ASP LEU LYS ARG PHE LEU LYS SEQRES 7 A 259 VAL LEU LYS LEU ALA ARG SER ARG ASP THR LEU VAL LEU SEQRES 8 A 259 ARG LYS GLY GLY GLU ASN PHE LEU GLU VAL GLY LEU LEU SEQRES 9 A 259 GLY ASP GLU ASN THR TRP PHE LYS LEU PRO LEU ILE ASP SEQRES 10 A 259 ALA ASN THR PRO GLU ILE GLU ILE PRO SER LEU PRO TRP SEQRES 11 A 259 THR VAL LYS ALA VAL VAL LEU ALA GLY ALA LEU LYS ARG SEQRES 12 A 259 ALA VAL LYS ALA ALA LYS LEU VAL SER ASP SER ILE TYR SEQRES 13 A 259 PHE MET ALA THR PRO GLU LYS LEU THR PHE LYS ALA GLU SEQRES 14 A 259 GLY ASN ASP SER GLU VAL ARG THR VAL LEU THR MET GLU SEQRES 15 A 259 ASP PRO GLY LEU LEU ASP LEU GLU HIS LYS MET THR LYS SEQRES 16 A 259 ALA LYS SER ALA TYR GLY VAL ALA TYR LEU GLU ASP ILE SEQRES 17 A 259 LEU ARG SER LEU ALA ASP ALA ASP GLU VAL ILE ILE ARG SEQRES 18 A 259 PHE GLY PHE ASP ILE PRO LEU LEU LEU LYS TYR MET VAL SEQRES 19 A 259 ARG ASP ALA GLY GLU VAL SER PHE LEU ILE ALA PRO ARG SEQRES 20 A 259 VAL GLU GLU GLY ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 259 MET THR PHE GLU ILE VAL PHE ASP SER ALA ARG GLU PHE SEQRES 2 B 259 GLU SER LEU ILE ALA THR LEU GLU LYS PHE PHE ASP GLU SEQRES 3 B 259 ALA VAL PHE GLN VAL ASN MET GLU GLY ILE GLN MET ARG SEQRES 4 B 259 ALA ILE ASP PRO SER ARG VAL VAL LEU VAL ASP LEU ASN SEQRES 5 B 259 LEU PRO GLU MET LEU PHE SER LYS TYR SER VAL GLU SER SEQRES 6 B 259 GLU GLU ALA ILE ALA PHE ASP LEU LYS ARG PHE LEU LYS SEQRES 7 B 259 VAL LEU LYS LEU ALA ARG SER ARG ASP THR LEU VAL LEU SEQRES 8 B 259 ARG LYS GLY GLY GLU ASN PHE LEU GLU VAL GLY LEU LEU SEQRES 9 B 259 GLY ASP GLU ASN THR TRP PHE LYS LEU PRO LEU ILE ASP SEQRES 10 B 259 ALA ASN THR PRO GLU ILE GLU ILE PRO SER LEU PRO TRP SEQRES 11 B 259 THR VAL LYS ALA VAL VAL LEU ALA GLY ALA LEU LYS ARG SEQRES 12 B 259 ALA VAL LYS ALA ALA LYS LEU VAL SER ASP SER ILE TYR SEQRES 13 B 259 PHE MET ALA THR PRO GLU LYS LEU THR PHE LYS ALA GLU SEQRES 14 B 259 GLY ASN ASP SER GLU VAL ARG THR VAL LEU THR MET GLU SEQRES 15 B 259 ASP PRO GLY LEU LEU ASP LEU GLU HIS LYS MET THR LYS SEQRES 16 B 259 ALA LYS SER ALA TYR GLY VAL ALA TYR LEU GLU ASP ILE SEQRES 17 B 259 LEU ARG SER LEU ALA ASP ALA ASP GLU VAL ILE ILE ARG SEQRES 18 B 259 PHE GLY PHE ASP ILE PRO LEU LEU LEU LYS TYR MET VAL SEQRES 19 B 259 ARG ASP ALA GLY GLU VAL SER PHE LEU ILE ALA PRO ARG SEQRES 20 B 259 VAL GLU GLU GLY ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 C 259 MET THR PHE GLU ILE VAL PHE ASP SER ALA ARG GLU PHE SEQRES 2 C 259 GLU SER LEU ILE ALA THR LEU GLU LYS PHE PHE ASP GLU SEQRES 3 C 259 ALA VAL PHE GLN VAL ASN MET GLU GLY ILE GLN MET ARG SEQRES 4 C 259 ALA ILE ASP PRO SER ARG VAL VAL LEU VAL ASP LEU ASN SEQRES 5 C 259 LEU PRO GLU MET LEU PHE SER LYS TYR SER VAL GLU SER SEQRES 6 C 259 GLU GLU ALA ILE ALA PHE ASP LEU LYS ARG PHE LEU LYS SEQRES 7 C 259 VAL LEU LYS LEU ALA ARG SER ARG ASP THR LEU VAL LEU SEQRES 8 C 259 ARG LYS GLY GLY GLU ASN PHE LEU GLU VAL GLY LEU LEU SEQRES 9 C 259 GLY ASP GLU ASN THR TRP PHE LYS LEU PRO LEU ILE ASP SEQRES 10 C 259 ALA ASN THR PRO GLU ILE GLU ILE PRO SER LEU PRO TRP SEQRES 11 C 259 THR VAL LYS ALA VAL VAL LEU ALA GLY ALA LEU LYS ARG SEQRES 12 C 259 ALA VAL LYS ALA ALA LYS LEU VAL SER ASP SER ILE TYR SEQRES 13 C 259 PHE MET ALA THR PRO GLU LYS LEU THR PHE LYS ALA GLU SEQRES 14 C 259 GLY ASN ASP SER GLU VAL ARG THR VAL LEU THR MET GLU SEQRES 15 C 259 ASP PRO GLY LEU LEU ASP LEU GLU HIS LYS MET THR LYS SEQRES 16 C 259 ALA LYS SER ALA TYR GLY VAL ALA TYR LEU GLU ASP ILE SEQRES 17 C 259 LEU ARG SER LEU ALA ASP ALA ASP GLU VAL ILE ILE ARG SEQRES 18 C 259 PHE GLY PHE ASP ILE PRO LEU LEU LEU LYS TYR MET VAL SEQRES 19 C 259 ARG ASP ALA GLY GLU VAL SER PHE LEU ILE ALA PRO ARG SEQRES 20 C 259 VAL GLU GLU GLY ARG SER HIS HIS HIS HIS HIS HIS HET SO4 A 260 5 HET SO4 A 261 5 HET SO4 A 262 5 HET SO4 B 260 5 HET SO4 B 261 5 HET SO4 C 260 5 HETNAM SO4 SULFATE ION FORMUL 4 SO4 6(O4 S 2-) FORMUL 10 HOH *71(H2 O) HELIX 1 1 SER A 9 LYS A 22 1 14 HELIX 2 2 MET A 56 PHE A 58 5 3 HELIX 3 3 LEU A 73 LYS A 81 1 9 HELIX 4 4 ALA A 138 SER A 152 1 15 HELIX 5 5 VAL A 202 ARG A 210 1 9 HELIX 6 6 SER B 9 PHE B 24 1 16 HELIX 7 7 MET B 56 PHE B 58 5 3 HELIX 8 8 LEU B 73 LYS B 81 1 9 HELIX 9 9 ALA B 138 LEU B 150 1 13 HELIX 10 10 VAL B 202 ARG B 210 1 9 HELIX 11 11 SER C 9 LYS C 22 1 14 HELIX 12 12 MET C 56 PHE C 58 5 3 HELIX 13 13 LEU C 73 LYS C 81 1 9 HELIX 14 14 ALA C 138 LEU C 150 1 13 HELIX 15 15 VAL C 202 ARG C 210 1 9 SHEET 1 A 9 LYS A 60 VAL A 63 0 SHEET 2 A 9 PHE A 3 PHE A 7 -1 N VAL A 6 O LYS A 60 SHEET 3 A 9 THR A 88 LYS A 93 -1 O LEU A 89 N PHE A 7 SHEET 4 A 9 PHE A 98 LEU A 104 -1 O GLU A 100 N ARG A 92 SHEET 5 A 9 ASN A 108 PRO A 114 -1 O THR A 109 N LEU A 103 SHEET 6 A 9 GLU B 174 THR B 180 -1 O ARG B 176 N TRP A 110 SHEET 7 A 9 LYS B 163 GLU B 169 -1 N PHE B 166 O THR B 177 SHEET 8 A 9 SER B 154 ALA B 159 -1 N MET B 158 O THR B 165 SHEET 9 A 9 ALA B 196 GLY B 201 -1 O SER B 198 N PHE B 157 SHEET 1 B 9 GLU A 67 ASP A 72 0 SHEET 2 B 9 GLU A 26 VAL A 31 -1 N PHE A 29 O ILE A 69 SHEET 3 B 9 GLY A 35 ILE A 41 -1 O GLN A 37 N GLN A 30 SHEET 4 B 9 VAL A 47 PRO A 54 -1 O LEU A 53 N ILE A 36 SHEET 5 B 9 GLY A 238 ILE A 244 -1 O SER A 241 N ASP A 50 SHEET 6 B 9 LEU A 228 VAL A 234 -1 N TYR A 232 O VAL A 240 SHEET 7 B 9 GLU A 217 PHE A 222 -1 N ARG A 221 O LEU A 229 SHEET 8 B 9 VAL A 132 LEU A 137 -1 N VAL A 136 O VAL A 218 SHEET 9 B 9 LEU A 186 HIS A 191 -1 O LEU A 187 N VAL A 135 SHEET 1 C 9 ALA A 196 GLY A 201 0 SHEET 2 C 9 SER A 154 ALA A 159 -1 N PHE A 157 O SER A 198 SHEET 3 C 9 LEU A 164 GLU A 169 -1 O LYS A 167 N TYR A 156 SHEET 4 C 9 GLU A 174 LEU A 179 -1 O LEU A 179 N LEU A 164 SHEET 5 C 9 ASN C 108 PRO C 114 -1 O TRP C 110 N ARG A 176 SHEET 6 C 9 PHE C 98 LEU C 104 -1 N VAL C 101 O PHE C 111 SHEET 7 C 9 THR C 88 LYS C 93 -1 N THR C 88 O LEU C 104 SHEET 8 C 9 PHE C 3 PHE C 7 -1 N ILE C 5 O LEU C 91 SHEET 9 C 9 TYR C 61 VAL C 63 -1 O SER C 62 N GLU C 4 SHEET 1 D 9 LYS B 60 VAL B 63 0 SHEET 2 D 9 PHE B 3 PHE B 7 -1 N VAL B 6 O LYS B 60 SHEET 3 D 9 THR B 88 LYS B 93 -1 O LEU B 91 N ILE B 5 SHEET 4 D 9 PHE B 98 LEU B 104 -1 O GLU B 100 N ARG B 92 SHEET 5 D 9 ASN B 108 PRO B 114 -1 O LEU B 113 N LEU B 99 SHEET 6 D 9 GLU C 174 THR C 180 -1 O ARG C 176 N TRP B 110 SHEET 7 D 9 LYS C 163 GLU C 169 -1 N LEU C 164 O LEU C 179 SHEET 8 D 9 SER C 154 ALA C 159 -1 N MET C 158 O THR C 165 SHEET 9 D 9 ALA C 196 GLY C 201 -1 O SER C 198 N PHE C 157 SHEET 1 E 9 ALA B 68 ASP B 72 0 SHEET 2 E 9 GLU B 26 VAL B 31 -1 N PHE B 29 O ILE B 69 SHEET 3 E 9 GLY B 35 ILE B 41 -1 O GLN B 37 N GLN B 30 SHEET 4 E 9 VAL B 47 PRO B 54 -1 O LEU B 53 N ILE B 36 SHEET 5 E 9 GLY B 238 ILE B 244 -1 O SER B 241 N ASP B 50 SHEET 6 E 9 LEU B 228 VAL B 234 -1 N LEU B 228 O ILE B 244 SHEET 7 E 9 GLU B 217 PHE B 222 -1 N ARG B 221 O LEU B 229 SHEET 8 E 9 VAL B 132 LEU B 137 -1 N ALA B 134 O ILE B 220 SHEET 9 E 9 LEU B 186 HIS B 191 -1 O GLU B 190 N LYS B 133 SHEET 1 F 9 GLU C 67 ASP C 72 0 SHEET 2 F 9 GLU C 26 VAL C 31 -1 N PHE C 29 O ILE C 69 SHEET 3 F 9 GLY C 35 ILE C 41 -1 O GLN C 37 N GLN C 30 SHEET 4 F 9 VAL C 47 PRO C 54 -1 O LEU C 53 N ILE C 36 SHEET 5 F 9 GLY C 238 ILE C 244 -1 O SER C 241 N ASP C 50 SHEET 6 F 9 LEU C 228 VAL C 234 -1 N LEU C 230 O PHE C 242 SHEET 7 F 9 GLU C 217 PHE C 222 -1 N ILE C 219 O LYS C 231 SHEET 8 F 9 VAL C 132 LEU C 137 -1 N VAL C 136 O VAL C 218 SHEET 9 F 9 LEU C 186 HIS C 191 -1 O GLU C 190 N LYS C 133 SITE 1 AC1 2 ALA A 213 ASP A 214 SITE 1 AC2 5 SER A 9 ARG A 11 SER A 85 ARG A 86 SITE 2 AC2 5 HOH A 268 SITE 1 AC3 2 GLU A 4 VAL A 90 SITE 1 AC4 2 ALA B 213 ASP B 214 SITE 1 AC5 4 SER B 9 ARG B 11 SER B 85 HOH B 278 SITE 1 AC6 2 SER C 9 SER C 85 CRYST1 120.480 136.270 123.970 90.00 90.00 90.00 C 2 2 21 24 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 0.008300 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007338 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008066 0.00000 MASTER 430 0 6 15 54 0 7 6 0 0 0 60 END