HEADER HYDROLASE 09-APR-15 4Z96 TITLE CRYSTAL STRUCTURE OF DNMT1 IN COMPLEX WITH USP7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 544-1067; COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN- COMPND 6 SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC- COMPND 7 PROCESSING PROTEASE 7; COMPND 8 EC: 3.4.19.12; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 1; COMPND 12 CHAIN: C; COMPND 13 FRAGMENT: UNP RESIDUES 1097-1129; COMPND 14 SYNONYM: DNMT1,CXXC-TYPE ZINC FINGER PROTEIN 9,DNA METHYLTRANSFERASE COMPND 15 HSAI,M.HSAI,MCMT; COMPND 16 EC: 2.1.1.37; COMPND 17 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: USP7, HAUSP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: DNMT1, AIM, CXXC9, DNMT; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS USP7, DNMT1, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.M.ZHANG,J.SONG REVDAT 2 27-SEP-23 4Z96 1 REMARK REVDAT 1 12-OCT-16 4Z96 0 JRNL AUTH Z.M.ZHANG,J.SONG JRNL TITL CRYSTAL STRUCTURE OF DNMT1 IN COMPLEX WITH USP7 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 29741 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.420 REMARK 3 FREE R VALUE TEST SET COUNT : 1909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.9657 - 6.8609 0.82 1870 135 0.1944 0.2578 REMARK 3 2 6.8609 - 5.4489 0.94 2072 140 0.2054 0.2574 REMARK 3 3 5.4489 - 4.7611 0.94 2061 136 0.1607 0.1802 REMARK 3 4 4.7611 - 4.3262 0.94 2042 141 0.1510 0.1964 REMARK 3 5 4.3262 - 4.0163 0.94 2012 137 0.1799 0.2232 REMARK 3 6 4.0163 - 3.7797 0.93 2017 140 0.1959 0.2389 REMARK 3 7 3.7797 - 3.5905 0.94 2008 135 0.2143 0.2483 REMARK 3 8 3.5905 - 3.4343 0.95 2026 141 0.2190 0.2947 REMARK 3 9 3.4343 - 3.3021 0.94 1999 139 0.2524 0.2988 REMARK 3 10 3.3021 - 3.1882 0.94 2011 133 0.2421 0.2822 REMARK 3 11 3.1882 - 3.0885 0.92 1967 139 0.2661 0.2826 REMARK 3 12 3.0885 - 3.0003 0.92 1956 135 0.2946 0.3470 REMARK 3 13 3.0003 - 2.9213 0.90 1916 129 0.3103 0.3363 REMARK 3 14 2.9213 - 2.8500 0.89 1875 129 0.3408 0.3907 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 4221 REMARK 3 ANGLE : 1.358 5722 REMARK 3 CHIRALITY : 0.054 630 REMARK 3 PLANARITY : 0.006 754 REMARK 3 DIHEDRAL : 15.487 1526 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 555 THROUGH 745 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.8054 -72.7443 -30.3720 REMARK 3 T TENSOR REMARK 3 T11: 0.8340 T22: 0.5027 REMARK 3 T33: 0.6010 T12: 0.0456 REMARK 3 T13: 0.2782 T23: 0.1185 REMARK 3 L TENSOR REMARK 3 L11: 4.4850 L22: 2.7816 REMARK 3 L33: 2.9247 L12: 1.5345 REMARK 3 L13: 2.2255 L23: 1.6198 REMARK 3 S TENSOR REMARK 3 S11: 0.2278 S12: -0.1286 S13: -0.3694 REMARK 3 S21: -0.3417 S22: 0.2092 S23: -0.3474 REMARK 3 S31: -0.1749 S32: 0.0922 S33: -0.4167 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 746 THROUGH 904 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.6486 -42.3489 -16.7222 REMARK 3 T TENSOR REMARK 3 T11: 0.7264 T22: 0.7208 REMARK 3 T33: 0.5629 T12: 0.0287 REMARK 3 T13: 0.0692 T23: -0.1467 REMARK 3 L TENSOR REMARK 3 L11: 5.9591 L22: 5.9044 REMARK 3 L33: 1.1318 L12: -5.3256 REMARK 3 L13: -2.6948 L23: 2.0001 REMARK 3 S TENSOR REMARK 3 S11: 0.1550 S12: -0.1171 S13: 0.4912 REMARK 3 S21: -0.3817 S22: 0.0813 S23: -0.2887 REMARK 3 S31: -0.2124 S32: -0.0974 S33: -0.1948 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 905 THROUGH 1083 ) REMARK 3 ORIGIN FOR THE GROUP (A): -52.3941 -9.2257 1.5534 REMARK 3 T TENSOR REMARK 3 T11: 1.0551 T22: 0.5838 REMARK 3 T33: 0.9337 T12: 0.2387 REMARK 3 T13: 0.3215 T23: -0.0297 REMARK 3 L TENSOR REMARK 3 L11: 2.6648 L22: 3.4775 REMARK 3 L33: 2.8414 L12: 0.8919 REMARK 3 L13: -1.6134 L23: 0.2326 REMARK 3 S TENSOR REMARK 3 S11: 0.8261 S12: 0.1661 S13: 1.1398 REMARK 3 S21: 0.0655 S22: -0.0298 S23: 0.2933 REMARK 3 S31: -0.9382 S32: -0.2701 S33: -0.5607 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1108 THROUGH 1115 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2515 -73.6539 -13.9921 REMARK 3 T TENSOR REMARK 3 T11: 0.6436 T22: 0.6429 REMARK 3 T33: 0.4792 T12: 0.1449 REMARK 3 T13: 0.0869 T23: 0.3983 REMARK 3 L TENSOR REMARK 3 L11: 7.3846 L22: 7.5459 REMARK 3 L33: 2.0057 L12: 1.0744 REMARK 3 L13: 1.8289 L23: -1.1992 REMARK 3 S TENSOR REMARK 3 S11: 0.1141 S12: 0.1031 S13: 0.8925 REMARK 3 S21: 0.8932 S22: -0.5064 S23: -0.0895 REMARK 3 S31: -0.5136 S32: 0.0817 S33: 0.1974 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4Z96 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 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 (%) : 94.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.68300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: 2YLM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH5.5, 10% REMARK 280 PEG6000, 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 102.00933 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 51.00467 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 51.00467 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 102.00933 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: 1330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A 554 REMARK 465 LYS A 984 REMARK 465 GLU A 985 REMARK 465 HIS A 1012 REMARK 465 LYS A 1033 REMARK 465 VAL A 1058 REMARK 465 ASN A 1069 REMARK 465 SER C 1097 REMARK 465 ASP C 1098 REMARK 465 TRP C 1099 REMARK 465 PRO C 1100 REMARK 465 ASN C 1101 REMARK 465 HIS C 1102 REMARK 465 ALA C 1103 REMARK 465 ARG C 1104 REMARK 465 SER C 1105 REMARK 465 PRO C 1106 REMARK 465 GLY C 1107 REMARK 465 GLY C 1116 REMARK 465 LYS C 1117 REMARK 465 GLY C 1118 REMARK 465 LYS C 1119 REMARK 465 PRO C 1120 REMARK 465 LYS C 1121 REMARK 465 SER C 1122 REMARK 465 GLN C 1123 REMARK 465 ALA C 1124 REMARK 465 CYS C 1125 REMARK 465 GLU C 1126 REMARK 465 PRO C 1127 REMARK 465 SER C 1128 REMARK 465 GLU C 1129 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 LYS A 590 CG CD CE NZ REMARK 470 GLU A 641 CG CD OE1 OE2 REMARK 470 ASN A 645 CG OD1 ND2 REMARK 470 LYS A 646 CG CD CE NZ REMARK 470 ASP A 666 CG OD1 OD2 REMARK 470 GLU A 668 CG CD OE1 OE2 REMARK 470 LEU A 669 CG CD1 CD2 REMARK 470 LYS A 678 CG CD CE NZ REMARK 470 LYS A 681 CG CD CE NZ REMARK 470 LYS A 695 CG CD CE NZ REMARK 470 ILE A 727 CG1 CG2 CD1 REMARK 470 ASP A 729 CG OD1 OD2 REMARK 470 ASP A 772 CG OD1 OD2 REMARK 470 GLU A 774 CG CD OE1 OE2 REMARK 470 LYS A 801 CG CD CE NZ REMARK 470 ASN A 805 CG OD1 ND2 REMARK 470 PHE A 820 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 824 CG CD CE NZ REMARK 470 GLN A 828 CG CD OE1 NE2 REMARK 470 LYS A 841 CG CD CE NZ REMARK 470 TYR A 845 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 846 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 847 CG OD1 OD2 REMARK 470 ARG A 854 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 869 CG CD CE NZ REMARK 470 ARG A 871 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 875 CG CD CE NZ REMARK 470 LYS A 882 CG CD CE NZ REMARK 470 LYS A 884 CD CE NZ REMARK 470 LYS A 914 CG CD CE NZ REMARK 470 GLU A 930 CG CD OE1 OE2 REMARK 470 LYS A 934 CG CD CE NZ REMARK 470 ASP A 981 CG OD1 OD2 REMARK 470 ILE A 982 CG1 CG2 CD1 REMARK 470 ASP A 983 CG OD1 OD2 REMARK 470 ASN A 986 CG OD1 ND2 REMARK 470 GLU A 998 OE1 OE2 REMARK 470 ILE A1011 CG1 CG2 CD1 REMARK 470 GLU A1015 CG CD OE1 OE2 REMARK 470 HIS A1016 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A1018 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1019 CG CD OE1 OE2 REMARK 470 MET A1021 CG SD CE REMARK 470 LYS A1022 CG CD CE NZ REMARK 470 GLN A1025 CG CD OE1 NE2 REMARK 470 SER A1026 OG REMARK 470 LEU A1028 CG CD1 CD2 REMARK 470 ASP A1029 CG OD1 OD2 REMARK 470 ILE A1030 CG1 CG2 CD1 REMARK 470 GLN A1031 CG CD OE1 NE2 REMARK 470 GLU A1034 CG CD OE1 OE2 REMARK 470 GLU A1036 CG CD OE1 OE2 REMARK 470 LYS A1037 CG CD CE NZ REMARK 470 LYS A1039 CG CD CE NZ REMARK 470 ILE A1042 CG1 CG2 CD1 REMARK 470 GLN A1049 CG CD OE1 NE2 REMARK 470 ILE A1051 CG1 CG2 CD1 REMARK 470 ASN A1052 CG OD1 ND2 REMARK 470 ASP A1054 CG OD1 OD2 REMARK 470 GLU A1055 CG CD OE1 OE2 REMARK 470 ASN A1059 CG OD1 ND2 REMARK 470 LEU A1060 CG CD1 CD2 REMARK 470 LYS A1061 CG CD CE NZ REMARK 470 GLU A1064 CG CD OE1 OE2 REMARK 470 ARG A1074 CG CD NE CZ NH1 NH2 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 OH TYR A 1050 OD2 ASP A 1080 2.17 REMARK 500 OG SER A 610 O PHE A 615 2.19 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 GLN A 828 N - CA - C ANGL. DEV. = 18.8 DEGREES REMARK 500 ARG A 829 N - CA - CB ANGL. DEV. = -18.9 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 ASP A 582 -161.08 52.34 REMARK 500 GLN A 619 31.54 -140.25 REMARK 500 ASN A 654 13.75 59.90 REMARK 500 ASP A 666 102.92 -51.69 REMARK 500 ASP A 750 41.54 -92.62 REMARK 500 PRO A 773 -18.89 -47.42 REMARK 500 ILE A 803 76.85 -119.43 REMARK 500 ASN A 815 -39.62 -24.18 REMARK 500 GLN A 828 -49.98 -23.75 REMARK 500 ASN A 831 -15.71 64.82 REMARK 500 GLN A 843 -71.17 -107.04 REMARK 500 ARG A 846 46.37 -90.66 REMARK 500 ASP A 847 100.03 -28.95 REMARK 500 ASN A 856 -9.94 -51.23 REMARK 500 PHE A 867 34.06 -96.71 REMARK 500 ASN A 900 -165.54 -60.17 REMARK 500 LYS A 934 -10.46 65.44 REMARK 500 ALA A 935 -176.00 -68.90 REMARK 500 GLU A 987 138.00 176.31 REMARK 500 HIS A 996 -100.02 -112.38 REMARK 500 LYS A 997 170.28 58.76 REMARK 500 GLU A 998 -76.39 -84.24 REMARK 500 LEU A1009 -165.19 -129.46 REMARK 500 GLU A1015 -160.60 178.79 REMARK 500 MET A1044 -160.28 -119.56 REMARK 500 ASN A1052 170.47 -58.42 REMARK 500 GLU A1053 31.60 -98.36 REMARK 500 ASP A1054 -64.34 -120.54 REMARK 500 LEU A1060 -126.03 -175.79 REMARK 500 GLU A1064 153.06 160.94 REMARK 500 PRO A1067 99.96 -60.60 REMARK 500 HIS A1081 -165.66 -163.23 REMARK 500 LYS C1111 60.34 -110.04 REMARK 500 LYS C1111 -68.89 -101.65 REMARK 500 LYS C1113 -77.56 -48.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 996 LYS A 997 130.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Z97 RELATED DB: PDB DBREF 4Z96 A 560 1083 UNP Q93009 UBP7_HUMAN 544 1067 DBREF 4Z96 C 1097 1129 UNP P26358 DNMT1_HUMAN 1097 1129 SEQADV 4Z96 SER A 554 UNP Q93009 EXPRESSION TAG SEQADV 4Z96 GLY A 555 UNP Q93009 EXPRESSION TAG SEQADV 4Z96 PRO A 556 UNP Q93009 EXPRESSION TAG SEQADV 4Z96 LEU A 557 UNP Q93009 EXPRESSION TAG SEQADV 4Z96 GLY A 558 UNP Q93009 EXPRESSION TAG SEQADV 4Z96 SER A 559 UNP Q93009 EXPRESSION TAG SEQADV 4Z96 SER C 1097 UNP P26358 GLU 1097 CONFLICT SEQADV 4Z96 TRP C 1099 UNP P26358 PRO 1099 CONFLICT SEQRES 1 A 530 SER GLY PRO LEU GLY SER GLU ALA HIS LEU TYR MET GLN SEQRES 2 A 530 VAL GLN ILE VAL ALA GLU ASP GLN PHE CYS GLY HIS GLN SEQRES 3 A 530 GLY ASN ASP MET TYR ASP GLU GLU LYS VAL LYS TYR THR SEQRES 4 A 530 VAL PHE LYS VAL LEU LYS ASN SER SER LEU ALA GLU PHE SEQRES 5 A 530 VAL GLN SER LEU SER GLN THR MET GLY PHE PRO GLN ASP SEQRES 6 A 530 GLN ILE ARG LEU TRP PRO MET GLN ALA ARG SER ASN GLY SEQRES 7 A 530 THR LYS ARG PRO ALA MET LEU ASP ASN GLU ALA ASP GLY SEQRES 8 A 530 ASN LYS THR MET ILE GLU LEU SER ASP ASN GLU ASN PRO SEQRES 9 A 530 TRP THR ILE PHE LEU GLU THR VAL ASP PRO GLU LEU ALA SEQRES 10 A 530 ALA SER GLY ALA THR LEU PRO LYS PHE ASP LYS ASP HIS SEQRES 11 A 530 ASP VAL MET LEU PHE LEU LYS MET TYR ASP PRO LYS THR SEQRES 12 A 530 ARG SER LEU ASN TYR CYS GLY HIS ILE TYR THR PRO ILE SEQRES 13 A 530 SER CYS LYS ILE ARG ASP LEU LEU PRO VAL MET CYS ASP SEQRES 14 A 530 ARG ALA GLY PHE ILE GLN ASP THR SER LEU ILE LEU TYR SEQRES 15 A 530 GLU GLU VAL LYS PRO ASN LEU THR GLU ARG ILE GLN ASP SEQRES 16 A 530 TYR ASP VAL SER LEU ASP LYS ALA LEU ASP GLU LEU MET SEQRES 17 A 530 ASP GLY ASP ILE ILE VAL PHE GLN LYS ASP ASP PRO GLU SEQRES 18 A 530 ASN ASP ASN SER GLU LEU PRO THR ALA LYS GLU TYR PHE SEQRES 19 A 530 ARG ASP LEU TYR HIS ARG VAL ASP VAL ILE PHE CYS ASP SEQRES 20 A 530 LYS THR ILE PRO ASN ASP PRO GLY PHE VAL VAL THR LEU SEQRES 21 A 530 SER ASN ARG MET ASN TYR PHE GLN VAL ALA LYS THR VAL SEQRES 22 A 530 ALA GLN ARG LEU ASN THR ASP PRO MET LEU LEU GLN PHE SEQRES 23 A 530 PHE LYS SER GLN GLY TYR ARG ASP GLY PRO GLY ASN PRO SEQRES 24 A 530 LEU ARG HIS ASN TYR GLU GLY THR LEU ARG ASP LEU LEU SEQRES 25 A 530 GLN PHE PHE LYS PRO ARG GLN PRO LYS LYS LEU TYR TYR SEQRES 26 A 530 GLN GLN LEU LYS MET LYS ILE THR ASP PHE GLU ASN ARG SEQRES 27 A 530 ARG SER PHE LYS CYS ILE TRP LEU ASN SER GLN PHE ARG SEQRES 28 A 530 GLU GLU GLU ILE THR LEU TYR PRO ASP LYS HIS GLY CYS SEQRES 29 A 530 VAL ARG ASP LEU LEU GLU GLU CYS LYS LYS ALA VAL GLU SEQRES 30 A 530 LEU GLY GLU LYS ALA SER GLY LYS LEU ARG LEU LEU GLU SEQRES 31 A 530 ILE VAL SER TYR LYS ILE ILE GLY VAL HIS GLN GLU ASP SEQRES 32 A 530 GLU LEU LEU GLU CYS LEU SER PRO ALA THR SER ARG THR SEQRES 33 A 530 PHE ARG ILE GLU GLU ILE PRO LEU ASP GLN VAL ASP ILE SEQRES 34 A 530 ASP LYS GLU ASN GLU MET LEU VAL THR VAL ALA HIS PHE SEQRES 35 A 530 HIS LYS GLU VAL PHE GLY THR PHE GLY ILE PRO PHE LEU SEQRES 36 A 530 LEU ARG ILE HIS GLN GLY GLU HIS PHE ARG GLU VAL MET SEQRES 37 A 530 LYS ARG ILE GLN SER LEU LEU ASP ILE GLN GLU LYS GLU SEQRES 38 A 530 PHE GLU LYS PHE LYS PHE ALA ILE VAL MET MET GLY ARG SEQRES 39 A 530 HIS GLN TYR ILE ASN GLU ASP GLU TYR GLU VAL ASN LEU SEQRES 40 A 530 LYS ASP PHE GLU PRO GLN PRO GLY ASN MET SER HIS PRO SEQRES 41 A 530 ARG PRO TRP LEU GLY LEU ASP HIS PHE ASN SEQRES 1 C 33 SER ASP TRP PRO ASN HIS ALA ARG SER PRO GLY ASN LYS SEQRES 2 C 33 GLY LYS GLY LYS GLY LYS GLY LYS GLY LYS PRO LYS SER SEQRES 3 C 33 GLN ALA CYS GLU PRO SER GLU HELIX 1 AA1 GLU A 560 HIS A 562 5 3 HELIX 2 AA2 ASP A 573 CYS A 576 5 4 HELIX 3 AA3 SER A 601 GLY A 614 1 14 HELIX 4 AA4 PRO A 616 ASP A 618 5 3 HELIX 5 AA5 ALA A 642 LYS A 646 5 5 HELIX 6 AA6 THR A 647 ASP A 653 1 7 HELIX 7 AA7 ASP A 666 SER A 672 1 7 HELIX 8 AA8 LYS A 712 ASP A 715 5 4 HELIX 9 AA9 LEU A 716 GLY A 725 1 10 HELIX 10 AB1 SER A 752 LEU A 757 1 6 HELIX 11 AB2 ASP A 772 SER A 778 5 7 HELIX 12 AB3 THR A 782 HIS A 792 1 11 HELIX 13 AB4 ASN A 818 ARG A 829 1 12 HELIX 14 AB5 ASP A 833 MET A 835 5 3 HELIX 15 AB6 THR A 860 LEU A 865 1 6 HELIX 16 AB7 LYS A 884 GLU A 889 1 6 HELIX 17 AB8 CYS A 917 LYS A 927 1 11 HELIX 18 AB9 LEU A 958 LEU A 962 5 5 HELIX 19 AC1 PRO A 976 VAL A 980 5 5 HELIX 20 AC2 HIS A 1016 ASP A 1029 1 14 SHEET 1 AA1 5 THR A 592 LEU A 597 0 SHEET 2 AA1 5 TYR A 564 ALA A 571 -1 N VAL A 567 O PHE A 594 SHEET 3 AA1 5 TRP A 658 THR A 664 1 O TRP A 658 N GLN A 568 SHEET 4 AA1 5 ILE A 620 ALA A 627 -1 N TRP A 623 O PHE A 661 SHEET 5 AA1 5 LYS A 633 PRO A 635 -1 O ARG A 634 N GLN A 626 SHEET 1 AA2 5 SER A 698 PRO A 708 0 SHEET 2 AA2 5 ASP A 684 ASP A 693 -1 N VAL A 685 O THR A 707 SHEET 3 AA2 5 ILE A 765 LYS A 770 1 O PHE A 768 N TYR A 692 SHEET 4 AA2 5 LEU A 732 LYS A 739 -1 N TYR A 735 O VAL A 767 SHEET 5 AA2 5 LEU A 742 ARG A 745 -1 O GLU A 744 N GLU A 736 SHEET 1 AA3 4 PHE A 809 SER A 814 0 SHEET 2 AA3 4 ARG A 793 ASP A 800 -1 N VAL A 796 O VAL A 811 SHEET 3 AA3 4 LYS A 874 GLN A 880 1 O LYS A 874 N ILE A 797 SHEET 4 AA3 4 LEU A 837 PHE A 840 -1 N PHE A 840 O TYR A 877 SHEET 1 AA4 5 GLU A 905 LEU A 910 0 SHEET 2 AA4 5 PHE A 894 LEU A 899 -1 N TRP A 898 O GLU A 906 SHEET 3 AA4 5 THR A 969 GLU A 974 1 O ILE A 972 N LEU A 899 SHEET 4 AA4 5 LEU A 939 VAL A 945 -1 N LEU A 942 O ARG A 971 SHEET 5 AA4 5 LYS A 948 VAL A 952 -1 O LYS A 948 N VAL A 945 SHEET 1 AA5 5 THR A1002 ARG A1010 0 SHEET 2 AA5 5 LEU A 989 PHE A 995 -1 N VAL A 992 O PHE A1007 SHEET 3 AA5 5 TRP A1076 ASP A1080 1 O LEU A1079 N PHE A 995 SHEET 4 AA5 5 LYS A1039 MET A1044 -1 N LYS A1039 O ASP A1080 SHEET 5 AA5 5 ARG A1047 ILE A1051 -1 O ARG A1047 N MET A1044 CISPEP 1 GLY A 555 PRO A 556 0 -5.55 CISPEP 2 ASN A 656 PRO A 657 0 11.74 CISPEP 3 HIS A 1072 PRO A 1073 0 5.04 CISPEP 4 ASN C 1108 LYS C 1109 0 10.77 CRYST1 124.044 124.044 153.014 90.00 90.00 120.00 P 32 2 1 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 0.008062 0.004654 0.000000 0.00000 SCALE2 0.000000 0.009309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006535 0.00000