PDB Short entry for 3DB3 HEADER LIGASE 30-MAY-08 3DB3 TITLE CRYSTAL STRUCTURE OF THE TANDEM TUDOR DOMAINS OF THE E3 UBIQUITIN- TITLE 2 PROTEIN LIGASE UHRF1 IN COMPLEX WITH TRIMETHYLATED HISTONE H3-K9 TITLE 3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UHRF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TANDEM TUDOR DOMAINS (UNP RESIDUES 126-285); 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 INVERTED CCAAT BOX-BINDING PROTEIN OF 90 KDA, TRANSCRIPTION FACTOR COMPND 8 ICBP90, NUCLEAR ZINC FINGER PROTEIN NP95, NUCLEAR PROTEIN 95, HUNP95, COMPND 9 RING FINGER PROTEIN 106; COMPND 10 EC: 6.3.2.-; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: TRIMETHYLATED HISTONE H3-K9 PEPTIDE; COMPND 14 CHAIN: B; COMPND 15 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: UHRF1, ICBP90, NP95, RNF106; 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: PET28-MHL; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: TRIMETHYLATED HISTONE PEPTIDE H3-K9 WAS CHEMICALLY SOURCE 14 SYNTHESIZED. THE SEQUENCE NATURALLY OCCURS IN HOMO SAPIENS (HUMAN) KEYWDS CELL CYCLE, DNA DAMAGE, DNA REPAIR, TANDEM TUDOR DOMAINS, LIGASE, KEYWDS 2 METAL BINDING, DNA REPLICATION, TRANSCRIPTIONAL SILENCING, KEYWDS 3 CHROMATIN, PHOSPHORYLATION, TRANSCRIPTION, TRANSCRIPTION REGULATION, KEYWDS 4 UBL CONJUGATION PATHWAY, ZINC-FINGER, STRUCTURAL GENOMICS, KEYWDS 5 STRUCTURAL GENOMICS CONSORTIUM, SGC, DNA-BINDING, METAL-BINDING, KEYWDS 6 NUCLEUS, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.R.WALKER,G.V.AVVAKUMOV,S.XUE,A.DONG,Y.LI,C.BOUNTRA,J.WEIGELT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,A.BOCHKAREV,S.DHE-PAGANON,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 4 18-APR-12 3DB3 1 JRNL VERSN REVDAT 3 13-APR-11 3DB3 1 JRNL REVDAT 2 24-FEB-09 3DB3 1 VERSN REVDAT 1 16-SEP-08 3DB3 0 JRNL AUTH N.NADY,A.LEMAK,J.R.WALKER,G.V.AVVAKUMOV,M.S.KARETA,M.ACHOUR, JRNL AUTH 2 S.XUE,S.DUAN,A.ALLALI-HASSANI,X.ZUO,Y.X.WANG,C.BRONNER, JRNL AUTH 3 F.CHEDIN,C.H.ARROWSMITH,S.DHE-PAGANON JRNL TITL RECOGNITION OF MULTIVALENT HISTONE STATES ASSOCIATED WITH JRNL TITL 2 HETEROCHROMATIN BY UHRF1 PROTEIN. JRNL REF J.BIOL.CHEM. V. 286 24300 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21489993 JRNL DOI 10.1074/JBC.M111.234104 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 31.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 8755 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 433 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 569 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 22 REMARK 3 BIN FREE R VALUE : 0.2230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1164 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.68000 REMARK 3 B22 (A**2) : -3.68000 REMARK 3 B33 (A**2) : 5.52000 REMARK 3 B12 (A**2) : -1.84000 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): 0.296 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.260 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.195 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.638 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1184 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1604 ; 1.298 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 140 ; 6.481 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 65 ;38.460 ;23.538 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 196 ;17.770 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;19.009 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 175 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 913 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 424 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 767 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 74 ; 0.147 ; 0.200 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): 14 ; 0.158 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.167 ; 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): 726 ; 1.424 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1144 ; 2.176 ; 4.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 523 ; 3.047 ; 5.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 460 ; 4.604 ; 7.000 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 : 8 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 127 A 137 REMARK 3 ORIGIN FOR THE GROUP (A): 28.0556 -0.6752 20.5866 REMARK 3 T TENSOR REMARK 3 T11: 0.2682 T22: -0.0187 REMARK 3 T33: 0.0335 T12: 0.0275 REMARK 3 T13: 0.0737 T23: -0.1192 REMARK 3 L TENSOR REMARK 3 L11: 2.4227 L22: 42.3760 REMARK 3 L33: 3.0403 L12: 5.7516 REMARK 3 L13: 0.5587 L23: -7.8179 REMARK 3 S TENSOR REMARK 3 S11: -0.7935 S12: -0.8142 S13: 0.2144 REMARK 3 S21: 1.4510 S22: 1.0206 S23: 2.7258 REMARK 3 S31: -0.6698 S32: -0.1124 S33: -0.2271 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 : A 138 A 149 REMARK 3 ORIGIN FOR THE GROUP (A): 33.0352 -6.6195 7.8505 REMARK 3 T TENSOR REMARK 3 T11: -0.0064 T22: 0.0356 REMARK 3 T33: 0.2101 T12: 0.0188 REMARK 3 T13: 0.0166 T23: -0.0549 REMARK 3 L TENSOR REMARK 3 L11: 4.1551 L22: 6.8888 REMARK 3 L33: 21.7632 L12: 1.2594 REMARK 3 L13: 4.8994 L23: 5.9467 REMARK 3 S TENSOR REMARK 3 S11: 0.2137 S12: -0.0139 S13: 0.1202 REMARK 3 S21: -0.0331 S22: -0.1573 S23: 0.2263 REMARK 3 S31: 0.1832 S32: -0.3221 S33: -0.0564 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 : A 150 A 162 REMARK 3 ORIGIN FOR THE GROUP (A): 32.4740 -3.1657 12.0750 REMARK 3 T TENSOR REMARK 3 T11: 0.1437 T22: -0.0196 REMARK 3 T33: 0.0160 T12: 0.0099 REMARK 3 T13: -0.0075 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 3.8692 L22: 11.2789 REMARK 3 L33: 9.5482 L12: 0.3710 REMARK 3 L13: -3.0512 L23: 5.4679 REMARK 3 S TENSOR REMARK 3 S11: 0.4256 S12: -0.1986 S13: 0.3873 REMARK 3 S21: 0.3700 S22: -0.0336 S23: -0.0255 REMARK 3 S31: -0.3589 S32: -0.1399 S33: -0.3920 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 : A 180 A 198 REMARK 3 ORIGIN FOR THE GROUP (A): 33.4396 -0.2793 9.5177 REMARK 3 T TENSOR REMARK 3 T11: 0.0819 T22: 0.0186 REMARK 3 T33: 0.1620 T12: 0.0019 REMARK 3 T13: -0.0030 T23: -0.0804 REMARK 3 L TENSOR REMARK 3 L11: 8.3427 L22: 5.9341 REMARK 3 L33: 9.6671 L12: -1.8807 REMARK 3 L13: -5.2850 L23: 0.5944 REMARK 3 S TENSOR REMARK 3 S11: 0.0145 S12: 0.1132 S13: -0.6022 REMARK 3 S21: 0.1757 S22: -0.1031 S23: 0.2898 REMARK 3 S31: -0.0301 S32: -0.4058 S33: 0.0886 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 : A 199 A 216 REMARK 3 ORIGIN FOR THE GROUP (A): 33.4613 -18.4890 8.7983 REMARK 3 T TENSOR REMARK 3 T11: 0.2462 T22: 0.0430 REMARK 3 T33: 0.0905 T12: 0.0279 REMARK 3 T13: -0.0463 T23: -0.0397 REMARK 3 L TENSOR REMARK 3 L11: 3.0946 L22: 4.8554 REMARK 3 L33: 1.5442 L12: 2.3640 REMARK 3 L13: 0.0699 L23: 2.2223 REMARK 3 S TENSOR REMARK 3 S11: 0.1010 S12: -0.2008 S13: -0.1076 REMARK 3 S21: 0.5993 S22: 0.0643 S23: -0.0475 REMARK 3 S31: 0.1797 S32: 0.0606 S33: -0.1653 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 : A 217 A 246 REMARK 3 ORIGIN FOR THE GROUP (A): 33.2903 -20.4219 -3.1923 REMARK 3 T TENSOR REMARK 3 T11: 0.0780 T22: 0.0795 REMARK 3 T33: 0.0927 T12: 0.0049 REMARK 3 T13: -0.0624 T23: -0.0336 REMARK 3 L TENSOR REMARK 3 L11: 5.1187 L22: 4.8493 REMARK 3 L33: 4.3799 L12: -0.2452 REMARK 3 L13: -0.4938 L23: 1.3318 REMARK 3 S TENSOR REMARK 3 S11: 0.0701 S12: 0.2857 S13: 0.0196 REMARK 3 S21: -0.1337 S22: -0.0298 S23: -0.0484 REMARK 3 S31: -0.2041 S32: 0.0792 S33: -0.0402 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 247 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): 35.5952 -32.8890 -7.2742 REMARK 3 T TENSOR REMARK 3 T11: 0.0438 T22: 0.0580 REMARK 3 T33: 0.1736 T12: -0.0466 REMARK 3 T13: -0.0412 T23: -0.0936 REMARK 3 L TENSOR REMARK 3 L11: 4.9679 L22: 15.3126 REMARK 3 L33: 2.4486 L12: -8.2626 REMARK 3 L13: -3.0329 L23: 4.0760 REMARK 3 S TENSOR REMARK 3 S11: 0.0105 S12: 0.2433 S13: -0.2258 REMARK 3 S21: -0.4986 S22: -0.2006 S23: -0.0044 REMARK 3 S31: -0.0290 S32: -0.0509 S33: 0.1901 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 259 A 283 REMARK 3 ORIGIN FOR THE GROUP (A): 31.6191 -20.0237 -0.4756 REMARK 3 T TENSOR REMARK 3 T11: 0.0980 T22: 0.0904 REMARK 3 T33: 0.1245 T12: -0.0721 REMARK 3 T13: -0.0022 T23: -0.0472 REMARK 3 L TENSOR REMARK 3 L11: 4.5652 L22: 5.2364 REMARK 3 L33: 8.1511 L12: -0.6866 REMARK 3 L13: 1.0698 L23: 1.9592 REMARK 3 S TENSOR REMARK 3 S11: -0.0230 S12: 0.0775 S13: 0.1244 REMARK 3 S21: -0.1184 S22: -0.1095 S23: 0.0842 REMARK 3 S31: -0.2454 S32: -0.4368 S33: 0.1325 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. REMARK 4 REMARK 4 3DB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB047816. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99987 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9214 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5200 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 (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 M SODIUM FORMATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 5.00, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 27.48800 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 13.74400 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.48800 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 13.74400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.4 KCAL/MOL 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 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 125 REMARK 465 MSE A 126 REMARK 465 ALA A 163 REMARK 465 PRO A 164 REMARK 465 SER A 165 REMARK 465 ARG A 166 REMARK 465 ASP A 167 REMARK 465 GLU A 168 REMARK 465 PRO A 169 REMARK 465 CYS A 170 REMARK 465 SER A 171 REMARK 465 SER A 172 REMARK 465 THR A 173 REMARK 465 SER A 174 REMARK 465 ARG A 175 REMARK 465 PRO A 176 REMARK 465 ALA A 177 REMARK 465 LEU A 178 REMARK 465 GLU A 179 REMARK 465 GLY A 284 REMARK 465 GLU A 285 REMARK 465 THR B 6 REMARK 465 ALA B 7 REMARK 465 THR B 11 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 TRP A 127 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 127 CZ3 CH2 REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 GLU A 131 CG CD OE1 OE2 REMARK 470 LYS A 136 CE NZ REMARK 470 ARG A 161 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 ASP A 181 CG OD1 OD2 REMARK 470 ARG A 202 CZ NH1 NH2 REMARK 470 ASP A 263 CG OD1 OD2 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 129 56.05 -112.29 REMARK 500 ASN A 138 -1.77 91.15 REMARK 500 THR A 249 -168.41 -110.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BI7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SRA DOMAIN OF E3 UBIQUITIN-PROTEIN REMARK 900 LIGASE UHRF1 REMARK 900 RELATED ID: 3CLZ RELATED DB: PDB REMARK 900 THE SET AND RING ASSOCIATED (SRA) DOMAIN OF UHRF1 BOUND TO REMARK 900 METHYLATED DNA REMARK 900 RELATED ID: 2FAZ RELATED DB: PDB REMARK 900 UBIQUITIN-LIKE DOMAIN OF HUMAN NUCLEAR ZINC FINGER PROTEIN REMARK 900 NP95 REMARK 900 RELATED ID: 3DB4 RELATED DB: PDB REMARK 900 STRUCTURE OF THE TANDEM TUDOR DOMAINS OF THE E3 UBIQUITIN- REMARK 900 PROTEIN LIGASE UHRF1 DBREF 3DB3 A 126 285 UNP Q96T88 UHRF1_HUMAN 126 285 DBREF 3DB3 B 6 11 UNP Q71DI3 H32_HUMAN 7 12 SEQADV 3DB3 GLY A 125 UNP Q96T88 EXPRESSION TAG SEQRES 1 A 161 GLY MSE TRP ASP GLU THR GLU LEU GLY LEU TYR LYS VAL SEQRES 2 A 161 ASN GLU TYR VAL ASP ALA ARG ASP THR ASN MSE GLY ALA SEQRES 3 A 161 TRP PHE GLU ALA GLN VAL VAL ARG VAL THR ARG LYS ALA SEQRES 4 A 161 PRO SER ARG ASP GLU PRO CYS SER SER THR SER ARG PRO SEQRES 5 A 161 ALA LEU GLU GLU ASP VAL ILE TYR HIS VAL LYS TYR ASP SEQRES 6 A 161 ASP TYR PRO GLU ASN GLY VAL VAL GLN MSE ASN SER ARG SEQRES 7 A 161 ASP VAL ARG ALA ARG ALA ARG THR ILE ILE LYS TRP GLN SEQRES 8 A 161 ASP LEU GLU VAL GLY GLN VAL VAL MSE LEU ASN TYR ASN SEQRES 9 A 161 PRO ASP ASN PRO LYS GLU ARG GLY PHE TRP TYR ASP ALA SEQRES 10 A 161 GLU ILE SER ARG LYS ARG GLU THR ARG THR ALA ARG GLU SEQRES 11 A 161 LEU TYR ALA ASN VAL VAL LEU GLY ASP ASP SER LEU ASN SEQRES 12 A 161 ASP CYS ARG ILE ILE PHE VAL ASP GLU VAL PHE LYS ILE SEQRES 13 A 161 GLU ARG PRO GLY GLU SEQRES 1 B 6 THR ALA ARG M3L SER THR MODRES 3DB3 MSE A 148 MET SELENOMETHIONINE MODRES 3DB3 MSE A 199 MET SELENOMETHIONINE MODRES 3DB3 MSE A 224 MET SELENOMETHIONINE MODRES 3DB3 M3L B 9 LYS N-TRIMETHYLLYSINE HET MSE A 148 8 HET MSE A 199 8 HET MSE A 224 8 HET M3L B 9 12 HETNAM MSE SELENOMETHIONINE HETNAM M3L N-TRIMETHYLLYSINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 HOH *73(H2 O) HELIX 1 1 TYR A 191 ASN A 194 5 4 HELIX 2 2 LYS A 213 LEU A 217 5 5 SHEET 1 A 5 VAL A 196 ASN A 200 0 SHEET 2 A 5 VAL A 182 TYR A 188 -1 N TYR A 184 O MSE A 199 SHEET 3 A 5 TRP A 151 ARG A 161 -1 N VAL A 157 O HIS A 185 SHEET 4 A 5 TYR A 140 ARG A 144 -1 N VAL A 141 O ALA A 154 SHEET 5 A 5 VAL A 204 ARG A 205 -1 O ARG A 205 N ASP A 142 SHEET 1 B 4 VAL A 222 TYR A 227 0 SHEET 2 B 4 PHE A 237 GLU A 248 -1 O ALA A 241 N VAL A 223 SHEET 3 B 4 ARG A 253 VAL A 260 -1 O GLU A 254 N ARG A 247 SHEET 4 B 4 SER A 265 ILE A 271 -1 O CYS A 269 N ALA A 257 LINK C ASN A 147 N MSE A 148 1555 1555 1.33 LINK C MSE A 148 N GLY A 149 1555 1555 1.33 LINK C GLN A 198 N MSE A 199 1555 1555 1.33 LINK C MSE A 199 N ASN A 200 1555 1555 1.33 LINK C VAL A 223 N MSE A 224 1555 1555 1.34 LINK C MSE A 224 N LEU A 225 1555 1555 1.32 LINK C ARG B 8 N M3L B 9 1555 1555 1.33 LINK C M3L B 9 N SER B 10 1555 1555 1.34 CRYST1 99.622 99.622 41.232 90.00 90.00 120.00 P 62 6 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 0.010038 0.005795 0.000000 0.00000 SCALE2 0.000000 0.011591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024253 0.00000