PDB Short entry for 5YD8 HEADER DNA BINDING PROTEIN 12-SEP-17 5YD8 TITLE CRYSTAL STRUCTURE OF HUMAN PCNA IN COMPLEX WITH APIM OF HUMAN ZRANB3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLIFERATING CELL NUCLEAR ANTIGEN; COMPND 3 CHAIN: Y, X, Z; COMPND 4 SYNONYM: PCNA,CYCLIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ZRANB3; COMPND 8 CHAIN: W, U, V; COMPND 9 FRAGMENT: UNP RESIDUES 1069-1079; COMPND 10 SYNONYM: ANNEALING HELICASE 2,AH2,ZINC FINGER RAN-BINDING DOMAIN- COMPND 11 CONTAINING PROTEIN 3; COMPND 12 EC: 3.6.4.-,3.1.-.-; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PCNA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS COMPLEX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.HASHIMOTO,R.TAGATA REVDAT 3 22-NOV-23 5YD8 1 REMARK REVDAT 2 18-DEC-19 5YD8 1 JRNL REVDAT 1 18-APR-18 5YD8 0 JRNL AUTH K.HARA,M.UCHIDA,R.TAGATA,H.YOKOYAMA,Y.ISHIKAWA,A.HISHIKI, JRNL AUTH 2 H.HASHIMOTO JRNL TITL STRUCTURE OF PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) BOUND JRNL TITL 2 TO AN APIM PEPTIDE REVEALS THE UNIVERSALITY OF PCNA JRNL TITL 3 INTERACTION. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 74 214 2018 JRNL REFN ESSN 2053-230X JRNL PMID 29633969 JRNL DOI 10.1107/S2053230X18003242 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 33604 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1771 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2481 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5888 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.66000 REMARK 3 B22 (A**2) : -0.66000 REMARK 3 B33 (A**2) : 2.16000 REMARK 3 B12 (A**2) : -0.33000 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): 0.399 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.262 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.224 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.777 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5961 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8037 ; 1.508 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 751 ; 6.573 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 244 ;46.332 ;25.328 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1115 ;17.563 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;22.034 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 960 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4292 ; 0.005 ; 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): 3043 ; 1.356 ; 3.247 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3781 ; 2.351 ; 4.856 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2918 ; 1.684 ; 3.459 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8291 ; 4.865 ;44.122 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 : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Y 1 Y 254 REMARK 3 ORIGIN FOR THE GROUP (A): 27.9252 -32.6701 -51.5118 REMARK 3 T TENSOR REMARK 3 T11: 0.1177 T22: 0.0929 REMARK 3 T33: 0.1696 T12: -0.0699 REMARK 3 T13: -0.0375 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 4.2671 L22: 2.5579 REMARK 3 L33: 0.3549 L12: -2.5468 REMARK 3 L13: -0.3376 L23: 0.1384 REMARK 3 S TENSOR REMARK 3 S11: -0.0053 S12: -0.0158 S13: -0.1043 REMARK 3 S21: 0.1292 S22: 0.0338 S23: -0.0279 REMARK 3 S31: 0.0915 S32: 0.0174 S33: -0.0285 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 1 X 255 REMARK 3 ORIGIN FOR THE GROUP (A): 24.5145 10.7028 -48.5881 REMARK 3 T TENSOR REMARK 3 T11: 0.0128 T22: 0.0342 REMARK 3 T33: 0.0807 T12: 0.0188 REMARK 3 T13: 0.0181 T23: 0.0236 REMARK 3 L TENSOR REMARK 3 L11: 4.7555 L22: 2.5448 REMARK 3 L33: 1.2361 L12: 2.0549 REMARK 3 L13: 0.6418 L23: 0.6282 REMARK 3 S TENSOR REMARK 3 S11: -0.0015 S12: -0.0043 S13: 0.0876 REMARK 3 S21: -0.0280 S22: 0.0279 S23: 0.0587 REMARK 3 S31: -0.0583 S32: -0.1288 S33: -0.0264 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Z 1 Z 255 REMARK 3 ORIGIN FOR THE GROUP (A): 64.6638 -8.0312 -50.0439 REMARK 3 T TENSOR REMARK 3 T11: 0.0401 T22: 0.1098 REMARK 3 T33: 0.1645 T12: -0.0059 REMARK 3 T13: -0.0034 T23: -0.0443 REMARK 3 L TENSOR REMARK 3 L11: 1.3677 L22: 6.0333 REMARK 3 L33: 0.9614 L12: -0.2825 REMARK 3 L13: -0.0584 L23: -1.2941 REMARK 3 S TENSOR REMARK 3 S11: 0.1022 S12: -0.0242 S13: 0.1906 REMARK 3 S21: -0.0778 S22: -0.0535 S23: 0.0280 REMARK 3 S31: -0.1289 S32: 0.0336 S33: -0.0487 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : W 1070 W 1077 REMARK 3 ORIGIN FOR THE GROUP (A): 75.3787 -15.6338 -36.5777 REMARK 3 T TENSOR REMARK 3 T11: 0.2072 T22: 0.1968 REMARK 3 T33: 0.1440 T12: 0.0142 REMARK 3 T13: -0.0534 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 11.2230 L22: 5.6474 REMARK 3 L33: 3.6414 L12: -1.6978 REMARK 3 L13: 4.6920 L23: 2.2960 REMARK 3 S TENSOR REMARK 3 S11: -0.0159 S12: -0.2305 S13: -0.1752 REMARK 3 S21: 0.5993 S22: 0.1567 S23: -0.1319 REMARK 3 S31: 0.3116 S32: -0.0333 S33: -0.1408 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : U 1069 U 1079 REMARK 3 ORIGIN FOR THE GROUP (A): 23.9942 23.9462 -35.6458 REMARK 3 T TENSOR REMARK 3 T11: 0.2200 T22: 0.2017 REMARK 3 T33: 0.1651 T12: 0.0214 REMARK 3 T13: 0.0492 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 8.6052 L22: 3.9828 REMARK 3 L33: 1.7147 L12: -0.2686 REMARK 3 L13: -0.5052 L23: 0.4733 REMARK 3 S TENSOR REMARK 3 S11: -0.0746 S12: -0.3700 S13: 0.0595 REMARK 3 S21: 0.2721 S22: 0.0247 S23: 0.2020 REMARK 3 S31: -0.1803 S32: -0.2094 S33: 0.0499 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : V 1071 V 1077 REMARK 3 ORIGIN FOR THE GROUP (A): 16.8844 -40.5886 -38.4725 REMARK 3 T TENSOR REMARK 3 T11: 0.3802 T22: 0.3486 REMARK 3 T33: 0.3257 T12: -0.0273 REMARK 3 T13: 0.0332 T23: 0.0686 REMARK 3 L TENSOR REMARK 3 L11: 14.1146 L22: 9.7006 REMARK 3 L33: 12.0797 L12: 0.2279 REMARK 3 L13: 9.2006 L23: -7.5303 REMARK 3 S TENSOR REMARK 3 S11: -0.3398 S12: -0.2726 S13: 0.0015 REMARK 3 S21: -0.1968 S22: 0.4697 S23: 0.1458 REMARK 3 S31: -0.0481 S32: -0.5585 S33: -0.1299 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005050. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40892 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <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: 2ZVM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 129.95200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.97600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.97600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 129.95200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: Y, V 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, U 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z, W REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY Y 83 REMARK 465 ASN Y 84 REMARK 465 GLU Y 85 REMARK 465 ASP Y 86 REMARK 465 PRO Y 106 REMARK 465 ASN Y 107 REMARK 465 GLN Y 108 REMARK 465 LEU Y 121 REMARK 465 ASP Y 122 REMARK 465 VAL Y 123 REMARK 465 GLU Y 124 REMARK 465 ILE Y 255 REMARK 465 GLU Y 256 REMARK 465 ASP Y 257 REMARK 465 GLU Y 258 REMARK 465 GLU Y 259 REMARK 465 GLY Y 260 REMARK 465 SER Y 261 REMARK 465 GLU X 124 REMARK 465 ASN X 187 REMARK 465 VAL X 188 REMARK 465 ASP X 189 REMARK 465 LYS X 190 REMARK 465 GLU X 191 REMARK 465 GLU X 192 REMARK 465 GLU X 256 REMARK 465 ASP X 257 REMARK 465 GLU X 258 REMARK 465 GLU X 259 REMARK 465 GLY X 260 REMARK 465 SER X 261 REMARK 465 SER Z 186 REMARK 465 ASN Z 187 REMARK 465 VAL Z 188 REMARK 465 ASP Z 189 REMARK 465 LYS Z 190 REMARK 465 GLU Z 191 REMARK 465 GLU Z 192 REMARK 465 ASP Z 243 REMARK 465 GLU Z 256 REMARK 465 ASP Z 257 REMARK 465 GLU Z 258 REMARK 465 GLU Z 259 REMARK 465 GLY Z 260 REMARK 465 SER Z 261 REMARK 465 GLY W 1069 REMARK 465 LYS W 1078 REMARK 465 LYS W 1079 REMARK 465 GLY V 1069 REMARK 465 SER V 1070 REMARK 465 LYS V 1078 REMARK 465 LYS V 1079 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 Y 104 -131.20 -155.54 REMARK 500 SER Y 186 -63.36 -128.74 REMARK 500 MET Y 244 -49.82 -133.92 REMARK 500 ASN X 95 64.71 65.70 REMARK 500 ALA X 96 98.90 -67.89 REMARK 500 GLN X 108 22.83 47.53 REMARK 500 ALA X 242 46.69 34.51 REMARK 500 GLN Z 8 -70.61 -85.64 REMARK 500 GLN Z 108 29.60 35.40 REMARK 500 ASP Z 122 38.97 -94.03 REMARK 500 ARG V1074 15.11 -69.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YD8 Y 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 5YD8 X 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 5YD8 Z 1 261 UNP P12004 PCNA_HUMAN 1 261 DBREF 5YD8 W 1069 1079 UNP Q5FWF4 ZRAB3_HUMAN 1069 1079 DBREF 5YD8 U 1069 1079 UNP Q5FWF4 ZRAB3_HUMAN 1069 1079 DBREF 5YD8 V 1069 1079 UNP Q5FWF4 ZRAB3_HUMAN 1069 1079 SEQRES 1 Y 261 MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE LEU LYS SEQRES 2 Y 261 LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN GLU ALA SEQRES 3 Y 261 CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU GLN SER SEQRES 4 Y 261 MET ASP SER SER HIS VAL SER LEU VAL GLN LEU THR LEU SEQRES 5 Y 261 ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP ARG ASN SEQRES 6 Y 261 LEU ALA MET GLY VAL ASN LEU THR SER MET SER LYS ILE SEQRES 7 Y 261 LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR LEU ARG SEQRES 8 Y 261 ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL PHE GLU SEQRES 9 Y 261 ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU MET LYS SEQRES 10 Y 261 LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE PRO GLU SEQRES 11 Y 261 GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER GLY GLU SEQRES 12 Y 261 PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE GLY ASP SEQRES 13 Y 261 ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL LYS PHE SEQRES 14 Y 261 SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE LYS LEU SEQRES 15 Y 261 SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU ALA VAL SEQRES 16 Y 261 THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR PHE ALA SEQRES 17 Y 261 LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR PRO LEU SEQRES 18 Y 261 SER SER THR VAL THR LEU SER MET SER ALA ASP VAL PRO SEQRES 19 Y 261 LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY HIS LEU SEQRES 20 Y 261 LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU GLU GLY SEQRES 21 Y 261 SER SEQRES 1 X 261 MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE LEU LYS SEQRES 2 X 261 LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN GLU ALA SEQRES 3 X 261 CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU GLN SER SEQRES 4 X 261 MET ASP SER SER HIS VAL SER LEU VAL GLN LEU THR LEU SEQRES 5 X 261 ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP ARG ASN SEQRES 6 X 261 LEU ALA MET GLY VAL ASN LEU THR SER MET SER LYS ILE SEQRES 7 X 261 LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR LEU ARG SEQRES 8 X 261 ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL PHE GLU SEQRES 9 X 261 ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU MET LYS SEQRES 10 X 261 LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE PRO GLU SEQRES 11 X 261 GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER GLY GLU SEQRES 12 X 261 PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE GLY ASP SEQRES 13 X 261 ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL LYS PHE SEQRES 14 X 261 SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE LYS LEU SEQRES 15 X 261 SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU ALA VAL SEQRES 16 X 261 THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR PHE ALA SEQRES 17 X 261 LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR PRO LEU SEQRES 18 X 261 SER SER THR VAL THR LEU SER MET SER ALA ASP VAL PRO SEQRES 19 X 261 LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY HIS LEU SEQRES 20 X 261 LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU GLU GLY SEQRES 21 X 261 SER SEQRES 1 Z 261 MET PHE GLU ALA ARG LEU VAL GLN GLY SER ILE LEU LYS SEQRES 2 Z 261 LYS VAL LEU GLU ALA LEU LYS ASP LEU ILE ASN GLU ALA SEQRES 3 Z 261 CYS TRP ASP ILE SER SER SER GLY VAL ASN LEU GLN SER SEQRES 4 Z 261 MET ASP SER SER HIS VAL SER LEU VAL GLN LEU THR LEU SEQRES 5 Z 261 ARG SER GLU GLY PHE ASP THR TYR ARG CYS ASP ARG ASN SEQRES 6 Z 261 LEU ALA MET GLY VAL ASN LEU THR SER MET SER LYS ILE SEQRES 7 Z 261 LEU LYS CYS ALA GLY ASN GLU ASP ILE ILE THR LEU ARG SEQRES 8 Z 261 ALA GLU ASP ASN ALA ASP THR LEU ALA LEU VAL PHE GLU SEQRES 9 Z 261 ALA PRO ASN GLN GLU LYS VAL SER ASP TYR GLU MET LYS SEQRES 10 Z 261 LEU MET ASP LEU ASP VAL GLU GLN LEU GLY ILE PRO GLU SEQRES 11 Z 261 GLN GLU TYR SER CYS VAL VAL LYS MET PRO SER GLY GLU SEQRES 12 Z 261 PHE ALA ARG ILE CYS ARG ASP LEU SER HIS ILE GLY ASP SEQRES 13 Z 261 ALA VAL VAL ILE SER CYS ALA LYS ASP GLY VAL LYS PHE SEQRES 14 Z 261 SER ALA SER GLY GLU LEU GLY ASN GLY ASN ILE LYS LEU SEQRES 15 Z 261 SER GLN THR SER ASN VAL ASP LYS GLU GLU GLU ALA VAL SEQRES 16 Z 261 THR ILE GLU MET ASN GLU PRO VAL GLN LEU THR PHE ALA SEQRES 17 Z 261 LEU ARG TYR LEU ASN PHE PHE THR LYS ALA THR PRO LEU SEQRES 18 Z 261 SER SER THR VAL THR LEU SER MET SER ALA ASP VAL PRO SEQRES 19 Z 261 LEU VAL VAL GLU TYR LYS ILE ALA ASP MET GLY HIS LEU SEQRES 20 Z 261 LYS TYR TYR LEU ALA PRO LYS ILE GLU ASP GLU GLU GLY SEQRES 21 Z 261 SER SEQRES 1 W 11 GLY SER ASP ILE THR ARG PHE LEU VAL LYS LYS SEQRES 1 U 11 GLY SER ASP ILE THR ARG PHE LEU VAL LYS LYS SEQRES 1 V 11 GLY SER ASP ILE THR ARG PHE LEU VAL LYS LYS FORMUL 7 HOH *45(H2 O) HELIX 1 AA1 GLY Y 9 LYS Y 20 1 12 HELIX 2 AA2 GLU Y 55 PHE Y 57 5 3 HELIX 3 AA3 LEU Y 72 LYS Y 80 1 9 HELIX 4 AA4 SER Y 141 SER Y 152 1 12 HELIX 5 AA5 LYS Y 190 ALA Y 194 5 5 HELIX 6 AA6 LEU Y 209 THR Y 216 1 8 HELIX 7 AA7 LYS Y 217 SER Y 222 5 6 HELIX 8 AA8 GLY X 9 ALA X 18 1 10 HELIX 9 AA9 GLU X 55 PHE X 57 5 3 HELIX 10 AB1 LEU X 72 LYS X 80 1 9 HELIX 11 AB2 SER X 141 HIS X 153 1 13 HELIX 12 AB3 LEU X 209 THR X 216 1 8 HELIX 13 AB4 LYS X 217 SER X 222 5 6 HELIX 14 AB5 GLY Z 9 ASP Z 21 1 13 HELIX 15 AB6 LEU Z 72 LYS Z 80 1 9 HELIX 16 AB7 SER Z 141 SER Z 152 1 12 HELIX 17 AB8 LEU Z 209 THR Z 216 1 8 HELIX 18 AB9 LYS Z 217 SER Z 222 5 6 HELIX 19 AC1 ILE W 1072 LEU W 1076 5 5 HELIX 20 AC2 ILE U 1072 LEU U 1076 5 5 HELIX 21 AC3 ILE V 1072 LEU V 1076 5 5 SHEET 1 AA1 9 THR Y 59 CYS Y 62 0 SHEET 2 AA1 9 PHE Y 2 LEU Y 6 -1 N GLU Y 3 O ARG Y 61 SHEET 3 AA1 9 ILE Y 88 ALA Y 92 -1 O ALA Y 92 N PHE Y 2 SHEET 4 AA1 9 THR Y 98 PHE Y 103 -1 O ALA Y 100 N ARG Y 91 SHEET 5 AA1 9 LYS Y 110 LYS Y 117 -1 O TYR Y 114 N LEU Y 101 SHEET 6 AA1 9 GLY Z 176 SER Z 183 -1 O LYS Z 181 N VAL Y 111 SHEET 7 AA1 9 GLY Z 166 GLY Z 173 -1 N VAL Z 167 O LEU Z 182 SHEET 8 AA1 9 ALA Z 157 CYS Z 162 -1 N VAL Z 159 O SER Z 170 SHEET 9 AA1 9 VAL Z 203 ALA Z 208 -1 O LEU Z 205 N ILE Z 160 SHEET 1 AA2 9 LEU Y 66 ASN Y 71 0 SHEET 2 AA2 9 GLU Y 25 SER Y 31 -1 N ALA Y 26 O VAL Y 70 SHEET 3 AA2 9 GLY Y 34 MET Y 40 -1 O ASN Y 36 N ASP Y 29 SHEET 4 AA2 9 SER Y 46 ARG Y 53 -1 O LEU Y 52 N VAL Y 35 SHEET 5 AA2 9 GLY Y 245 LEU Y 251 -1 O LYS Y 248 N GLN Y 49 SHEET 6 AA2 9 LEU Y 235 ILE Y 241 -1 N ILE Y 241 O GLY Y 245 SHEET 7 AA2 9 THR Y 224 MET Y 229 -1 N THR Y 226 O GLU Y 238 SHEET 8 AA2 9 CYS Y 135 PRO Y 140 -1 N VAL Y 137 O LEU Y 227 SHEET 9 AA2 9 THR Y 196 MET Y 199 -1 O THR Y 196 N LYS Y 138 SHEET 1 AA3 9 VAL Y 203 ALA Y 208 0 SHEET 2 AA3 9 ALA Y 157 ALA Y 163 -1 N ILE Y 160 O LEU Y 205 SHEET 3 AA3 9 GLY Y 166 SER Y 172 -1 O LYS Y 168 N SER Y 161 SHEET 4 AA3 9 GLY Y 176 SER Y 183 -1 O ILE Y 180 N PHE Y 169 SHEET 5 AA3 9 LYS X 110 LYS X 117 -1 O ASP X 113 N ASN Y 179 SHEET 6 AA3 9 THR X 98 GLU X 104 -1 N LEU X 101 O TYR X 114 SHEET 7 AA3 9 ILE X 87 ALA X 92 -1 N ARG X 91 O ALA X 100 SHEET 8 AA3 9 PHE X 2 LEU X 6 -1 N LEU X 6 O ILE X 88 SHEET 9 AA3 9 THR X 59 CYS X 62 -1 O ARG X 61 N GLU X 3 SHEET 1 AA4 9 LEU X 66 ASN X 71 0 SHEET 2 AA4 9 GLU X 25 SER X 31 -1 N ILE X 30 O LEU X 66 SHEET 3 AA4 9 GLY X 34 MET X 40 -1 O ASN X 36 N ASP X 29 SHEET 4 AA4 9 SER X 46 ARG X 53 -1 O VAL X 48 N SER X 39 SHEET 5 AA4 9 GLY X 245 LEU X 251 -1 O LYS X 248 N GLN X 49 SHEET 6 AA4 9 LEU X 235 ILE X 241 -1 N ILE X 241 O GLY X 245 SHEET 7 AA4 9 THR X 224 MET X 229 -1 N SER X 228 O VAL X 236 SHEET 8 AA4 9 CYS X 135 PRO X 140 -1 N VAL X 137 O LEU X 227 SHEET 9 AA4 9 THR X 196 MET X 199 -1 O GLU X 198 N VAL X 136 SHEET 1 AA5 2 LEU X 126 GLY X 127 0 SHEET 2 AA5 2 VAL U1077 LYS U1078 -1 O VAL U1077 N GLY X 127 SHEET 1 AA6 9 VAL X 203 ALA X 208 0 SHEET 2 AA6 9 ALA X 157 CYS X 162 -1 N ILE X 160 O LEU X 205 SHEET 3 AA6 9 GLY X 166 SER X 172 -1 O LYS X 168 N SER X 161 SHEET 4 AA6 9 GLY X 176 SER X 183 -1 O LEU X 182 N VAL X 167 SHEET 5 AA6 9 LYS Z 110 LYS Z 117 -1 O VAL Z 111 N LYS X 181 SHEET 6 AA6 9 THR Z 98 GLU Z 104 -1 N LEU Z 99 O MET Z 116 SHEET 7 AA6 9 ILE Z 87 ALA Z 92 -1 N ARG Z 91 O ALA Z 100 SHEET 8 AA6 9 PHE Z 2 LEU Z 6 -1 N LEU Z 6 O ILE Z 88 SHEET 9 AA6 9 PHE Z 57 CYS Z 62 -1 O ARG Z 61 N GLU Z 3 SHEET 1 AA7 9 LEU Z 66 ASN Z 71 0 SHEET 2 AA7 9 GLU Z 25 SER Z 31 -1 N ILE Z 30 O LEU Z 66 SHEET 3 AA7 9 GLY Z 34 MET Z 40 -1 O ASN Z 36 N ASP Z 29 SHEET 4 AA7 9 SER Z 46 ARG Z 53 -1 O VAL Z 48 N SER Z 39 SHEET 5 AA7 9 GLY Z 245 LEU Z 251 -1 O LYS Z 248 N GLN Z 49 SHEET 6 AA7 9 LEU Z 235 LYS Z 240 -1 N VAL Z 237 O TYR Z 249 SHEET 7 AA7 9 THR Z 224 MET Z 229 -1 N THR Z 226 O GLU Z 238 SHEET 8 AA7 9 CYS Z 135 PRO Z 140 -1 N VAL Z 137 O LEU Z 227 SHEET 9 AA7 9 THR Z 196 MET Z 199 -1 O GLU Z 198 N VAL Z 136 SSBOND 1 CYS Y 135 CYS Y 162 1555 1555 2.05 SSBOND 2 CYS X 135 CYS X 162 1555 1555 1.96 SSBOND 3 CYS Z 135 CYS Z 162 1555 1555 2.05 CRYST1 83.678 83.678 194.928 90.00 90.00 120.00 P 32 2 1 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011951 0.006900 0.000000 0.00000 SCALE2 0.000000 0.013799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005130 0.00000