PDB Short entry for 3PTA HEADER TRANSFERASE/DNA 02-DEC-10 3PTA TITLE CRYSTAL STRUCTURE OF HUMAN DNMT1(646-1600) IN COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 646-1600; COMPND 5 SYNONYM: DNMT1, CXXC-TYPE ZINC FINGER PROTEIN 9, DNA COMPND 6 METHYLTRANSFERASE HSAI, DNA MTASE HSAI, M.HSAI, MCMT; COMPND 7 EC: 2.1.1.37; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'- COMPND 11 D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'- COMPND 16 D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3'); COMPND 17 CHAIN: C; COMPND 18 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: DNMT1, AIM, CXXC9, DNMT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS DNMT1, MAINTENANCE DNA METHYLATION, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.SONG,D.J.PATEL REVDAT 3 21-FEB-24 3PTA 1 REMARK SEQADV LINK REVDAT 2 30-MAR-11 3PTA 1 JRNL SOURCE REVDAT 1 29-DEC-10 3PTA 0 JRNL AUTH J.SONG,O.RECHKOBLIT,T.H.BESTOR,D.J.PATEL JRNL TITL STRUCTURE OF DNMT1-DNA COMPLEX REVEALS A ROLE FOR JRNL TITL 2 AUTOINHIBITION IN MAINTENANCE DNA METHYLATION. JRNL REF SCIENCE V. 331 1036 2011 JRNL REFN ISSN 0036-8075 JRNL PMID 21163962 JRNL DOI 10.1126/SCIENCE.1195380 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 18554 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.257 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 954 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7186 REMARK 3 NUCLEIC ACID ATOMS : 773 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 0 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.020 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062789. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2827 REMARK 200 MONOCHROMATOR : SI MIRRORS REMARK 200 OPTICS : NULL 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 : 19075 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG 20,000, 0.1M MES, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 81.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 81.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 645 REMARK 465 ASN A 646 REMARK 465 GLU A 852 REMARK 465 SER A 853 REMARK 465 LEU A 854 REMARK 465 LEU A 855 REMARK 465 GLU A 856 REMARK 465 GLY A 857 REMARK 465 ASP A 858 REMARK 465 ASP A 859 REMARK 465 VAL A 956 REMARK 465 LYS A 957 REMARK 465 ARG A 958 REMARK 465 PRO A 959 REMARK 465 ARG A 960 REMARK 465 ASP A 978 REMARK 465 TYR A 979 REMARK 465 ILE A 980 REMARK 465 LYS A 981 REMARK 465 GLY A 982 REMARK 465 SER A 983 REMARK 465 ASN A 1108 REMARK 465 LYS A 1109 REMARK 465 GLY A 1110 REMARK 465 LYS A 1111 REMARK 465 GLY A 1112 REMARK 465 LYS A 1113 REMARK 465 GLY A 1114 REMARK 465 LYS A 1115 REMARK 465 GLY A 1116 REMARK 465 LYS A 1117 REMARK 465 GLY A 1118 REMARK 465 LYS A 1119 REMARK 465 PRO A 1120 REMARK 465 LYS A 1121 REMARK 465 SER A 1122 REMARK 465 GLN A 1123 REMARK 465 ALA A 1124 REMARK 465 CYS A 1125 REMARK 465 GLU A 1126 REMARK 465 PRO A 1127 REMARK 465 SER A 1128 REMARK 465 GLU A 1129 REMARK 465 PRO A 1130 REMARK 465 GLU A 1131 REMARK 465 ILE A 1132 REMARK 465 GLU A 1133 REMARK 465 ILE A 1134 REMARK 465 GLU A 1480 REMARK 465 ALA A 1481 REMARK 465 GLY A 1482 REMARK 465 LYS A 1483 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 PRO A1407 C - N - CA ANGL. DEV. = 12.0 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 VAL A 655 -70.40 -111.92 REMARK 500 CYS A 656 153.57 -35.68 REMARK 500 CYS A 664 -88.78 -44.02 REMARK 500 LYS A 668 -71.06 -49.69 REMARK 500 ARG A 681 1.22 -69.75 REMARK 500 LYS A 683 78.65 56.17 REMARK 500 ARG A 690 98.74 -54.08 REMARK 500 ASP A 700 -151.96 -105.19 REMARK 500 GLU A 703 92.88 -6.19 REMARK 500 ASN A 708 -168.65 -73.35 REMARK 500 GLU A 711 115.90 -35.87 REMARK 500 MET A 712 142.55 -175.58 REMARK 500 PRO A 715 -110.06 -66.54 REMARK 500 LYS A 717 -25.17 -33.42 REMARK 500 GLN A 720 -170.20 69.23 REMARK 500 LYS A 722 77.73 51.26 REMARK 500 ASP A 741 -121.12 -87.74 REMARK 500 LYS A 749 -168.70 -127.02 REMARK 500 ALA A 754 -25.69 81.21 REMARK 500 PRO A 767 -161.97 -65.38 REMARK 500 SER A 770 6.98 -65.47 REMARK 500 SER A 787 -31.09 -156.49 REMARK 500 ASP A 818 48.65 -75.94 REMARK 500 LEU A 825 -45.84 -15.84 REMARK 500 SER A 826 -9.57 -54.31 REMARK 500 ASN A 842 66.95 -105.03 REMARK 500 ALA A 844 20.46 -58.06 REMARK 500 LYS A 861 -17.07 -140.80 REMARK 500 GLN A 866 -15.49 -148.91 REMARK 500 THR A 885 -160.00 -115.20 REMARK 500 ASN A 888 0.51 -167.83 REMARK 500 LYS A 891 29.85 -140.60 REMARK 500 SER A 895 -72.32 -52.87 REMARK 500 GLU A 906 -70.28 -69.65 REMARK 500 LEU A 911 -129.50 -120.84 REMARK 500 LEU A 914 -42.31 -131.23 REMARK 500 ASN A 929 34.95 35.15 REMARK 500 LYS A 951 104.05 -38.88 REMARK 500 LEU A 952 116.72 -39.27 REMARK 500 GLU A 962 156.41 -48.80 REMARK 500 ASP A 965 97.93 -50.54 REMARK 500 TYR A 969 76.28 -113.61 REMARK 500 PRO A 970 -74.97 -51.67 REMARK 500 GLU A 971 3.88 -61.88 REMARK 500 TYR A 976 -73.11 -64.41 REMARK 500 PRO A 990 177.36 -59.63 REMARK 500 PRO A1002 -177.54 -57.13 REMARK 500 SER A1005 115.86 -24.92 REMARK 500 ASN A1006 -38.69 122.00 REMARK 500 ASN A1010 112.21 -177.12 REMARK 500 REMARK 500 THIS ENTRY HAS 92 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A1405 0.09 SIDE CHAIN REMARK 500 DC C 21 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1476 SG REMARK 620 2 CYS A1478 SG 92.7 REMARK 620 3 CYS A1485 SG 124.0 99.6 REMARK 620 4 HIS A1502 NE2 125.7 91.8 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 653 SG REMARK 620 2 CYS A 656 SG 95.1 REMARK 620 3 CYS A 659 SG 131.2 96.4 REMARK 620 4 CYS A 691 SG 112.3 129.0 96.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 793 NE2 REMARK 620 2 CYS A 820 SG 96.7 REMARK 620 3 CYS A 893 SG 128.9 114.9 REMARK 620 4 CYS A 896 SG 105.4 116.9 95.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 5 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 667 SG REMARK 620 2 CYS A 686 SG 137.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PT6 RELATED DB: PDB REMARK 900 RELATED ID: 3PT9 RELATED DB: PDB DBREF 3PTA A 646 1600 UNP P26358 DNMT1_HUMAN 646 1600 DBREF 3PTA B 1 19 PDB 3PTA 3PTA 1 19 DBREF 3PTA C 20 38 PDB 3PTA 3PTA 20 38 SEQADV 3PTA SER A 645 UNP P26358 EXPRESSION TAG SEQRES 1 A 956 SER ASN ALA PHE LYS ARG ARG ARG CYS GLY VAL CYS GLU SEQRES 2 A 956 VAL CYS GLN GLN PRO GLU CYS GLY LYS CYS LYS ALA CYS SEQRES 3 A 956 LYS ASP MET VAL LYS PHE GLY GLY SER GLY ARG SER LYS SEQRES 4 A 956 GLN ALA CYS GLN GLU ARG ARG CYS PRO ASN MET ALA MET SEQRES 5 A 956 LYS GLU ALA ASP ASP ASP GLU GLU VAL ASP ASP ASN ILE SEQRES 6 A 956 PRO GLU MET PRO SER PRO LYS LYS MET HIS GLN GLY LYS SEQRES 7 A 956 LYS LYS LYS GLN ASN LYS ASN ARG ILE SER TRP VAL GLY SEQRES 8 A 956 GLU ALA VAL LYS THR ASP GLY LYS LYS SER TYR TYR LYS SEQRES 9 A 956 LYS VAL CYS ILE ASP ALA GLU THR LEU GLU VAL GLY ASP SEQRES 10 A 956 CYS VAL SER VAL ILE PRO ASP ASP SER SER LYS PRO LEU SEQRES 11 A 956 TYR LEU ALA ARG VAL THR ALA LEU TRP GLU ASP SER SER SEQRES 12 A 956 ASN GLY GLN MET PHE HIS ALA HIS TRP PHE CYS ALA GLY SEQRES 13 A 956 THR ASP THR VAL LEU GLY ALA THR SER ASP PRO LEU GLU SEQRES 14 A 956 LEU PHE LEU VAL ASP GLU CYS GLU ASP MET GLN LEU SER SEQRES 15 A 956 TYR ILE HIS SER LYS VAL LYS VAL ILE TYR LYS ALA PRO SEQRES 16 A 956 SER GLU ASN TRP ALA MET GLU GLY GLY MET ASP PRO GLU SEQRES 17 A 956 SER LEU LEU GLU GLY ASP ASP GLY LYS THR TYR PHE TYR SEQRES 18 A 956 GLN LEU TRP TYR ASP GLN ASP TYR ALA ARG PHE GLU SER SEQRES 19 A 956 PRO PRO LYS THR GLN PRO THR GLU ASP ASN LYS PHE LYS SEQRES 20 A 956 PHE CYS VAL SER CYS ALA ARG LEU ALA GLU MET ARG GLN SEQRES 21 A 956 LYS GLU ILE PRO ARG VAL LEU GLU GLN LEU GLU ASP LEU SEQRES 22 A 956 ASP SER ARG VAL LEU TYR TYR SER ALA THR LYS ASN GLY SEQRES 23 A 956 ILE LEU TYR ARG VAL GLY ASP GLY VAL TYR LEU PRO PRO SEQRES 24 A 956 GLU ALA PHE THR PHE ASN ILE LYS LEU SER SER PRO VAL SEQRES 25 A 956 LYS ARG PRO ARG LYS GLU PRO VAL ASP GLU ASP LEU TYR SEQRES 26 A 956 PRO GLU HIS TYR ARG LYS TYR SER ASP TYR ILE LYS GLY SEQRES 27 A 956 SER ASN LEU ASP ALA PRO GLU PRO TYR ARG ILE GLY ARG SEQRES 28 A 956 ILE LYS GLU ILE PHE CYS PRO LYS LYS SER ASN GLY ARG SEQRES 29 A 956 PRO ASN GLU THR ASP ILE LYS ILE ARG VAL ASN LYS PHE SEQRES 30 A 956 TYR ARG PRO GLU ASN THR HIS LYS SER THR PRO ALA SER SEQRES 31 A 956 TYR HIS ALA ASP ILE ASN LEU LEU TYR TRP SER ASP GLU SEQRES 32 A 956 GLU ALA VAL VAL ASP PHE LYS ALA VAL GLN GLY ARG CYS SEQRES 33 A 956 THR VAL GLU TYR GLY GLU ASP LEU PRO GLU CYS VAL GLN SEQRES 34 A 956 VAL TYR SER MET GLY GLY PRO ASN ARG PHE TYR PHE LEU SEQRES 35 A 956 GLU ALA TYR ASN ALA LYS SER LYS SER PHE GLU ASP PRO SEQRES 36 A 956 PRO ASN HIS ALA ARG SER PRO GLY ASN LYS GLY LYS GLY SEQRES 37 A 956 LYS GLY LYS GLY LYS GLY LYS PRO LYS SER GLN ALA CYS SEQRES 38 A 956 GLU PRO SER GLU PRO GLU ILE GLU ILE LYS LEU PRO LYS SEQRES 39 A 956 LEU ARG THR LEU ASP VAL PHE SER GLY CYS GLY GLY LEU SEQRES 40 A 956 SER GLU GLY PHE HIS GLN ALA GLY ILE SER ASP THR LEU SEQRES 41 A 956 TRP ALA ILE GLU MET TRP ASP PRO ALA ALA GLN ALA PHE SEQRES 42 A 956 ARG LEU ASN ASN PRO GLY SER THR VAL PHE THR GLU ASP SEQRES 43 A 956 CYS ASN ILE LEU LEU LYS LEU VAL MET ALA GLY GLU THR SEQRES 44 A 956 THR ASN SER ARG GLY GLN ARG LEU PRO GLN LYS GLY ASP SEQRES 45 A 956 VAL GLU MET LEU CYS GLY GLY PRO PRO CYS GLN GLY PHE SEQRES 46 A 956 SER GLY MET ASN ARG PHE ASN SER ARG THR TYR SER LYS SEQRES 47 A 956 PHE LYS ASN SER LEU VAL VAL SER PHE LEU SER TYR CYS SEQRES 48 A 956 ASP TYR TYR ARG PRO ARG PHE PHE LEU LEU GLU ASN VAL SEQRES 49 A 956 ARG ASN PHE VAL SER PHE LYS ARG SER MET VAL LEU LYS SEQRES 50 A 956 LEU THR LEU ARG CYS LEU VAL ARG MET GLY TYR GLN CYS SEQRES 51 A 956 THR PHE GLY VAL LEU GLN ALA GLY GLN TYR GLY VAL ALA SEQRES 52 A 956 GLN THR ARG ARG ARG ALA ILE ILE LEU ALA ALA ALA PRO SEQRES 53 A 956 GLY GLU LYS LEU PRO LEU PHE PRO GLU PRO LEU HIS VAL SEQRES 54 A 956 PHE ALA PRO ARG ALA CYS GLN LEU SER VAL VAL VAL ASP SEQRES 55 A 956 ASP LYS LYS PHE VAL SER ASN ILE THR ARG LEU SER SER SEQRES 56 A 956 GLY PRO PHE ARG THR ILE THR VAL ARG ASP THR MET SER SEQRES 57 A 956 ASP LEU PRO GLU VAL ARG ASN GLY ALA SER ALA LEU GLU SEQRES 58 A 956 ILE SER TYR ASN GLY GLU PRO GLN SER TRP PHE GLN ARG SEQRES 59 A 956 GLN LEU ARG GLY ALA GLN TYR GLN PRO ILE LEU ARG ASP SEQRES 60 A 956 HIS ILE CYS LYS ASP MET SER ALA LEU VAL ALA ALA ARG SEQRES 61 A 956 MET ARG HIS ILE PRO LEU ALA PRO GLY SER ASP TRP ARG SEQRES 62 A 956 ASP LEU PRO ASN ILE GLU VAL ARG LEU SER ASP GLY THR SEQRES 63 A 956 MET ALA ARG LYS LEU ARG TYR THR HIS HIS ASP ARG LYS SEQRES 64 A 956 ASN GLY ARG SER SER SER GLY ALA LEU ARG GLY VAL CYS SEQRES 65 A 956 SER CYS VAL GLU ALA GLY LYS ALA CYS ASP PRO ALA ALA SEQRES 66 A 956 ARG GLN PHE ASN THR LEU ILE PRO TRP CYS LEU PRO HIS SEQRES 67 A 956 THR GLY ASN ARG HIS ASN HIS TRP ALA GLY LEU TYR GLY SEQRES 68 A 956 ARG LEU GLU TRP ASP GLY PHE PHE SER THR THR VAL THR SEQRES 69 A 956 ASN PRO GLU PRO MET GLY LYS GLN GLY ARG VAL LEU HIS SEQRES 70 A 956 PRO GLU GLN HIS ARG VAL VAL SER VAL ARG GLU CYS ALA SEQRES 71 A 956 ARG SER GLN GLY PHE PRO ASP THR TYR ARG LEU PHE GLY SEQRES 72 A 956 ASN ILE LEU ASP LYS HIS ARG GLN VAL GLY ASN ALA VAL SEQRES 73 A 956 PRO PRO PRO LEU ALA LYS ALA ILE GLY LEU GLU ILE LYS SEQRES 74 A 956 LEU CYS MET LEU ALA LYS ALA SEQRES 1 B 19 DT DC DC DC DG DT DG DA DG DC DC DT DC SEQRES 2 B 19 DC DG DC DA DG DG SEQRES 1 C 19 DC DC DT DG DC DG DG DA DG DG DC DT DC SEQRES 2 C 19 DA DC DG DG DG DA HET SAH A1601 26 HET ZN A 1 1 HET ZN A 2 1 HET ZN A 3 1 HET ZN A 5 1 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 ZN 4(ZN 2+) HELIX 1 1 CYS A 656 GLN A 661 1 6 HELIX 2 2 CYS A 667 ASP A 672 1 6 HELIX 3 3 MET A 673 GLY A 677 5 5 HELIX 4 4 THR A 801 THR A 803 5 3 HELIX 5 5 CYS A 893 ILE A 907 1 15 HELIX 6 6 TYR A 969 LYS A 975 5 7 HELIX 7 7 ARG A 1023 THR A 1027 5 5 HELIX 8 8 SER A 1030 HIS A 1036 5 7 HELIX 9 9 LYS A 1054 VAL A 1056 5 3 HELIX 10 10 CYS A 1071 GLY A 1078 1 8 HELIX 11 11 PRO A 1100 ARG A 1104 5 5 HELIX 12 12 GLY A 1149 GLY A 1159 1 11 HELIX 13 13 TRP A 1170 ASN A 1181 1 12 HELIX 14 14 ASP A 1190 MET A 1199 1 10 HELIX 15 15 ASN A 1236 LYS A 1244 1 9 HELIX 16 16 VAL A 1248 CYS A 1255 1 8 HELIX 17 17 ASN A 1270 ARG A 1276 5 7 HELIX 18 18 SER A 1277 MET A 1290 1 14 HELIX 19 19 GLY A 1302 GLY A 1305 5 4 HELIX 20 20 ALA A 1335 CYS A 1339 5 5 HELIX 21 21 THR A 1366 MET A 1371 1 6 HELIX 22 22 SER A 1394 ARG A 1401 1 8 HELIX 23 23 SER A 1418 HIS A 1427 1 10 HELIX 24 24 ASP A 1435 LEU A 1439 5 5 HELIX 25 25 ASP A 1486 ARG A 1490 5 5 HELIX 26 26 TRP A 1498 ASN A 1505 1 8 HELIX 27 27 ARG A 1506 ALA A 1511 5 6 HELIX 28 28 SER A 1549 GLN A 1557 1 9 HELIX 29 29 ASN A 1568 ALA A 1579 1 12 HELIX 30 30 PRO A 1581 LEU A 1597 1 17 SHEET 1 A 3 ILE A 731 VAL A 734 0 SHEET 2 A 3 LYS A 749 ILE A 752 -1 O CYS A 751 N SER A 732 SHEET 3 A 3 GLU A 755 GLU A 758 -1 O GLU A 755 N ILE A 752 SHEET 1 B 7 ILE A 828 VAL A 832 0 SHEET 2 B 7 CYS A 762 VAL A 765 -1 N SER A 764 O HIS A 829 SHEET 3 B 7 TYR A 775 GLU A 784 -1 O TYR A 775 N VAL A 765 SHEET 4 B 7 GLN A 790 ALA A 799 -1 O HIS A 793 N THR A 780 SHEET 5 B 7 GLU A 813 GLN A 824 -1 O PHE A 815 N CYS A 798 SHEET 6 B 7 PHE A 864 ASP A 870 1 O TYR A 869 N LEU A 816 SHEET 7 B 7 ILE A 835 TYR A 836 1 N ILE A 835 O TYR A 865 SHEET 1 C 7 ILE A 828 VAL A 832 0 SHEET 2 C 7 CYS A 762 VAL A 765 -1 N SER A 764 O HIS A 829 SHEET 3 C 7 TYR A 775 GLU A 784 -1 O TYR A 775 N VAL A 765 SHEET 4 C 7 GLN A 790 ALA A 799 -1 O HIS A 793 N THR A 780 SHEET 5 C 7 GLU A 813 GLN A 824 -1 O PHE A 815 N CYS A 798 SHEET 6 C 7 PHE A 864 ASP A 870 1 O TYR A 869 N LEU A 816 SHEET 7 C 7 ARG A 875 GLU A 877 -1 O GLU A 877 N TRP A 868 SHEET 1 D 3 ARG A 909 VAL A 910 0 SHEET 2 D 3 SER A 925 LYS A 928 -1 O THR A 927 N ARG A 909 SHEET 3 D 3 ILE A 931 ARG A 934 -1 O ILE A 931 N LYS A 928 SHEET 1 E 7 GLN A 913 LEU A 917 0 SHEET 2 E 7 ARG A 920 TYR A 923 -1 O LEU A 922 N LEU A 914 SHEET 3 E 7 ARG A 992 PRO A1002 -1 O ILE A 999 N TYR A 923 SHEET 4 E 7 GLY A 938 LEU A 941 -1 N LEU A 941 O ARG A 992 SHEET 5 E 7 ARG A1059 TYR A1064 -1 O CYS A1060 N GLY A 938 SHEET 6 E 7 ARG A1082 ASN A1090 1 O PHE A1083 N THR A1061 SHEET 7 E 7 SER A1095 GLU A1097 -1 O SER A1095 N ASN A1090 SHEET 1 F 7 GLN A 913 LEU A 917 0 SHEET 2 F 7 ARG A 920 TYR A 923 -1 O LEU A 922 N LEU A 914 SHEET 3 F 7 ARG A 992 PRO A1002 -1 O ILE A 999 N TYR A 923 SHEET 4 F 7 LYS A1015 TYR A1022 -1 O ARG A1017 N LYS A 997 SHEET 5 F 7 LEU A1041 ASP A1052 -1 O TYR A1043 N TYR A1022 SHEET 6 F 7 ARG A1082 ASN A1090 1 O TYR A1089 N TRP A1044 SHEET 7 F 7 SER A1095 GLU A1097 -1 O SER A1095 N ASN A1090 SHEET 1 G 7 THR A1185 PHE A1187 0 SHEET 2 G 7 SER A1161 ILE A1167 1 N ALA A1166 O PHE A1187 SHEET 3 G 7 LEU A1139 VAL A1144 1 N THR A1141 O LEU A1164 SHEET 4 G 7 MET A1219 GLY A1222 1 O MET A1219 N LEU A1142 SHEET 5 G 7 PHE A1262 VAL A1268 1 O PHE A1262 N LEU A1220 SHEET 6 G 7 ARG A1311 ALA A1318 -1 O ALA A1313 N ASN A1267 SHEET 7 G 7 GLN A1293 GLN A1300 -1 N GLN A1293 O ALA A1318 SHEET 1 H 2 VAL A1343 VAL A1344 0 SHEET 2 H 2 LYS A1349 PHE A1350 -1 O PHE A1350 N VAL A1343 SHEET 1 I 2 GLU A1385 ILE A1386 0 SHEET 2 I 2 LEU A1409 ARG A1410 -1 O LEU A1409 N ILE A1386 SHEET 1 J 2 VAL A1444 ARG A1445 0 SHEET 2 J 2 MET A1451 ALA A1452 -1 O ALA A1452 N VAL A1444 LINK ZN ZN A 1 SG CYS A1476 1555 1555 2.39 LINK ZN ZN A 1 SG CYS A1478 1555 1555 2.52 LINK ZN ZN A 1 SG CYS A1485 1555 1555 2.88 LINK ZN ZN A 1 NE2 HIS A1502 1555 1555 2.24 LINK ZN ZN A 2 SG CYS A 653 1555 1555 2.33 LINK ZN ZN A 2 SG CYS A 656 1555 1555 2.29 LINK ZN ZN A 2 SG CYS A 659 1555 1555 2.44 LINK ZN ZN A 2 SG CYS A 691 1555 1555 2.41 LINK ZN ZN A 3 NE2 HIS A 793 1555 1555 2.31 LINK ZN ZN A 3 SG CYS A 820 1555 1555 2.39 LINK ZN ZN A 3 SG CYS A 893 1555 1555 2.44 LINK ZN ZN A 3 SG CYS A 896 1555 1555 2.32 LINK ZN ZN A 5 SG CYS A 667 1555 1555 2.29 LINK ZN ZN A 5 SG CYS A 686 1555 1555 2.66 SITE 1 AC1 16 PHE A1145 SER A1146 GLY A1147 GLY A1150 SITE 2 AC1 16 LEU A1151 GLU A1168 MET A1169 TRP A1170 SITE 3 AC1 16 GLU A1189 CYS A1191 PRO A1225 LEU A1247 SITE 4 AC1 16 GLU A1266 ASN A1578 ALA A1579 VAL A1580 SITE 1 AC2 4 CYS A1476 CYS A1478 CYS A1485 HIS A1502 SITE 1 AC3 4 CYS A 653 CYS A 656 CYS A 659 CYS A 691 SITE 1 AC4 4 HIS A 793 CYS A 820 CYS A 893 CYS A 896 SITE 1 AC5 5 CYS A 664 CYS A 667 CYS A 670 CYS A 686 SITE 2 AC5 5 GLN A 687 CRYST1 162.800 87.900 113.900 90.00 97.20 90.00 C 1 2 1 4 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 0.006143 0.000000 0.000776 0.00000 SCALE2 0.000000 0.011377 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008849 0.00000