HEADER LIGASE 19-MAR-08 2ZKF TITLE CRYSTAL STRUCTURE OF THE SRA DOMAIN OF MOUSE NP95 IN COMPLEX WITH TITLE 2 HEMI-METHYLATED CPG DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UHRF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 404-613; COMPND 5 SYNONYM: UBIQUITIN-LIKE PHD AND RING FINGER DOMAIN-CONTAINING PROTEIN COMPND 6 1, UBIQUITIN-LIKE-CONTAINING PHD AND RING FINGER DOMAINS PROTEIN 1, COMPND 7 NUCLEAR ZINC FINGER PROTEIN NP95, NUCLEAR PROTEIN 95; COMPND 8 EC: 6.3.2.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (5'-D(P*DCP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DAP*DGP*DA)- COMPND 12 3'); COMPND 13 CHAIN: C; COMPND 14 SYNONYM: OLIGONUCLEOTIDES CONTAINING HEMI-METHYLATED CPG SITE; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: DNA (5'-D(*DCP*DTP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DGP*DA)- COMPND 18 3'); COMPND 19 CHAIN: D; COMPND 20 SYNONYM: OLIGONUCLEOTIDES CONTAINING HEMI-METHYLATED CPG SITE; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: UHRF1, NP95; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: NUCLEOTIDE SYNTHESIS; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: NUCLEOTIDE SYNTHESIS KEYWDS PROTEIN-DNA INTERACTION, CELL CYCLE, DEVELOPMENTAL PROTEIN, DNA KEYWDS 2 DAMAGE, DNA REPAIR, DNA-BINDING, LIGASE, METAL-BINDING, NUCLEUS, KEYWDS 3 PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION REGULATION, UBL KEYWDS 4 CONJUGATION PATHWAY, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR K.ARITA,M.ARIYOSHI,H.TOCHIO,Y.NAKAMURA,M.SHIRAKAWA REVDAT 6 01-NOV-23 2ZKF 1 REMARK REVDAT 5 10-NOV-21 2ZKF 1 SEQADV LINK REVDAT 4 13-JUL-11 2ZKF 1 VERSN REVDAT 3 24-FEB-09 2ZKF 1 VERSN REVDAT 2 14-OCT-08 2ZKF 1 JRNL REVDAT 1 09-SEP-08 2ZKF 0 JRNL AUTH K.ARITA,M.ARIYOSHI,H.TOCHIO,Y.NAKAMURA,M.SHIRAKAWA JRNL TITL RECOGNITION OF HEMI-METHYLATED DNA BY THE SRA PROTEIN UHRF1 JRNL TITL 2 BY A BASE-FLIPPING MECHANISM JRNL REF NATURE V. 455 818 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18772891 JRNL DOI 10.1038/NATURE07249 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10594 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 532 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 751 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1641 REMARK 3 NUCLEIC ACID ATOMS : 451 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 51.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.30000 REMARK 3 B22 (A**2) : 0.30000 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): 0.568 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.320 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.235 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.210 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2187 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1392 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3052 ; 2.012 ; 2.210 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3352 ; 1.017 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 208 ; 7.127 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;36.009 ;22.588 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 271 ;18.832 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;19.128 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 313 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2158 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 412 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 462 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1559 ; 0.228 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 991 ; 0.204 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1070 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 88 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.120 ; 0.200 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): 10 ; 0.175 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 28 ; 0.301 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.254 ; 0.200 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): 1290 ; 0.788 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 432 ; 0.133 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1647 ; 1.057 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1523 ; 1.584 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1405 ; 2.482 ; 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 : 3 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 : A 406 A 613 REMARK 3 ORIGIN FOR THE GROUP (A): 17.9604 -11.9558 -15.5114 REMARK 3 T TENSOR REMARK 3 T11: 0.0235 T22: 0.0696 REMARK 3 T33: 0.0462 T12: -0.0165 REMARK 3 T13: -0.0024 T23: 0.0295 REMARK 3 L TENSOR REMARK 3 L11: 1.1093 L22: 0.6688 REMARK 3 L33: 1.5104 L12: -0.2186 REMARK 3 L13: 0.6751 L23: -0.3538 REMARK 3 S TENSOR REMARK 3 S11: -0.0695 S12: 0.0123 S13: -0.0025 REMARK 3 S21: 0.0294 S22: 0.0577 S23: 0.0101 REMARK 3 S31: -0.0639 S32: -0.0938 S33: 0.0118 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 : C 2 C 12 REMARK 3 ORIGIN FOR THE GROUP (A): 15.8382 -12.4519 3.1956 REMARK 3 T TENSOR REMARK 3 T11: -0.0022 T22: 0.0534 REMARK 3 T33: -0.0149 T12: 0.1038 REMARK 3 T13: -0.0193 T23: 0.0721 REMARK 3 L TENSOR REMARK 3 L11: 8.4447 L22: 2.8805 REMARK 3 L33: 7.0388 L12: 2.1812 REMARK 3 L13: 3.3948 L23: 1.6345 REMARK 3 S TENSOR REMARK 3 S11: 0.4351 S12: -0.4207 S13: -0.3283 REMARK 3 S21: 0.3449 S22: -0.5185 S23: -0.2732 REMARK 3 S31: 0.3286 S32: -0.6326 S33: 0.0834 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 : D 2 D 12 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9351 -9.2740 2.5323 REMARK 3 T TENSOR REMARK 3 T11: -0.0505 T22: 0.1143 REMARK 3 T33: 0.0384 T12: 0.0545 REMARK 3 T13: -0.0551 T23: 0.0260 REMARK 3 L TENSOR REMARK 3 L11: 4.6436 L22: 2.3266 REMARK 3 L33: 5.6048 L12: 3.1949 REMARK 3 L13: 1.5355 L23: 1.8134 REMARK 3 S TENSOR REMARK 3 S11: 0.0143 S12: -0.4614 S13: 0.1231 REMARK 3 S21: -0.0820 S22: -0.4539 S23: -0.2371 REMARK 3 S31: -0.2356 S32: -0.5252 S33: 0.4396 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2ZKF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000028083. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : UNDULATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11160 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.17100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 ENTRY 2ZKD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS-PROPANE (PH7.5), 0.2M REMARK 280 SODIUM FLUORIDE, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 91.15450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.43900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.43900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.57725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.43900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.43900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 136.73175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.43900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.43900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.57725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.43900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.43900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 136.73175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 91.15450 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: 4350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 A 43 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 SER A 404 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC C 2 P DC C 2 OP3 -0.121 REMARK 500 DC C 5 O3' DC C 5 C3' -0.050 REMARK 500 DG C 11 O3' DG C 11 C3' -0.053 REMARK 500 DT D 10 O3' DT D 10 C3' -0.042 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 448 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 596 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 596 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 DC C 2 OP1 - P - OP2 ANGL. DEV. = -14.3 DEGREES REMARK 500 DA C 3 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG C 6 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG C 7 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA C 10 O4' - C1' - N9 ANGL. DEV. = -6.1 DEGREES REMARK 500 DA C 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT D 3 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT D 5 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT D 5 C4 - C5 - C7 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT D 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG D 8 O4' - C1' - N9 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG D 8 N3 - C2 - N2 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG D 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT D 10 P - O5' - C5' ANGL. DEV. = -11.4 DEGREES REMARK 500 DT D 10 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG D 11 O4' - C1' - N9 ANGL. DEV. = -6.8 DEGREES REMARK 500 DG D 11 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DA D 12 O4' - C1' - N9 ANGL. DEV. = 3.4 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 THR A 413 -158.80 -130.58 REMARK 500 ILE A 417 -60.85 -9.44 REMARK 500 ASN A 421 41.15 -105.41 REMARK 500 ASP A 460 -60.29 -136.94 REMARK 500 ASN A 508 -130.36 57.58 REMARK 500 SER A 519 139.91 -178.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZKD RELATED DB: PDB REMARK 900 RELATED ID: 2ZKE RELATED DB: PDB REMARK 900 RELATED ID: 2ZKG RELATED DB: PDB DBREF 2ZKF C 2 12 PDB 2ZKF 2ZKF 2 12 DBREF 2ZKF D 2 12 PDB 2ZKF 2ZKF 2 12 DBREF 2ZKF A 404 613 UNP Q8VDF2 UHRF1_MOUSE 404 613 SEQADV 2ZKF SER A 404 UNP Q8VDF2 LYS 404 ENGINEERED MUTATION SEQRES 1 A 210 SER GLY MET ALA CYS VAL GLY ARG THR THR GLU CYS THR SEQRES 2 A 210 ILE VAL PRO ALA ASN HIS PHE GLY PRO ILE PRO GLY VAL SEQRES 3 A 210 PRO VAL GLY THR MET TRP ARG PHE ARG VAL GLN VAL SER SEQRES 4 A 210 GLU SER GLY VAL HIS ARG PRO HIS VAL ALA GLY ILE HIS SEQRES 5 A 210 GLY ARG SER ASN ASP GLY ALA TYR SER LEU VAL LEU ALA SEQRES 6 A 210 GLY GLY TYR GLU ASP ASP VAL ASP ASN GLY ASN TYR PHE SEQRES 7 A 210 THR TYR THR GLY SER GLY GLY ARG ASP LEU SER GLY ASN SEQRES 8 A 210 LYS ARG THR ALA GLY GLN SER SER ASP GLN LYS LEU THR SEQRES 9 A 210 ASN ASN ASN ARG ALA LEU ALA LEU ASN CYS HIS SER PRO SEQRES 10 A 210 ILE ASN GLU LYS GLY ALA GLU ALA GLU ASP TRP ARG GLN SEQRES 11 A 210 GLY LYS PRO VAL ARG VAL VAL ARG ASN MET LYS GLY GLY SEQRES 12 A 210 LYS HIS SER LYS TYR ALA PRO ALA GLU GLY ASN ARG TYR SEQRES 13 A 210 ASP GLY ILE TYR LYS VAL VAL LYS TYR TRP PRO GLU ARG SEQRES 14 A 210 GLY LYS SER GLY PHE LEU VAL TRP ARG TYR LEU LEU ARG SEQRES 15 A 210 ARG ASP ASP THR GLU PRO GLU PRO TRP THR ARG GLU GLY SEQRES 16 A 210 LYS ASP ARG THR ARG GLN LEU GLY LEU THR MET GLN TYR SEQRES 17 A 210 PRO GLU SEQRES 1 C 11 DC DA DC DC DG DG DA DT DA DG DA SEQRES 1 D 11 DC DT DA DT DC 5CM DG DG DT DG DA MODRES 2ZKF 5CM D 7 DC HET 5CM D 7 20 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 3 5CM C10 H16 N3 O7 P FORMUL 4 HOH *45(H2 O) HELIX 1 1 PHE A 437 SER A 444 1 8 HELIX 2 2 THR A 507 ASN A 516 1 10 HELIX 3 3 ASP A 530 GLY A 534 5 5 HELIX 4 4 LYS A 544 HIS A 548 5 5 HELIX 5 5 THR A 595 LEU A 605 1 11 SHEET 1 A 5 MET A 434 TRP A 435 0 SHEET 2 A 5 ASN A 557 ARG A 572 -1 O ASN A 557 N TRP A 435 SHEET 3 A 5 LEU A 578 ARG A 586 -1 O ARG A 581 N TRP A 569 SHEET 4 A 5 TYR A 480 THR A 484 -1 N TYR A 483 O TYR A 582 SHEET 5 A 5 VAL A 475 ASP A 476 -1 N VAL A 475 O THR A 482 SHEET 1 B 5 ILE A 454 ARG A 457 0 SHEET 2 B 5 GLY A 461 LEU A 467 -1 O SER A 464 N HIS A 455 SHEET 3 B 5 VAL A 537 ASN A 542 1 O VAL A 540 N LEU A 465 SHEET 4 B 5 ASN A 557 ARG A 572 -1 O TYR A 563 N VAL A 537 SHEET 5 B 5 ALA A 526 GLU A 527 -1 N ALA A 526 O TYR A 568 LINK O3' DC D 6 P 5CM D 7 1555 1555 1.59 LINK O3' 5CM D 7 P DG D 8 1555 1555 1.60 CRYST1 58.878 58.878 182.309 90.00 90.00 90.00 P 41 21 2 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 0.016984 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005485 0.00000