HEADER TRANSFERASE 31-AUG-16 5GUV TITLE THE CRYSTAL STRUCTURE OF MOUSE DNMT1 (731-1602) MUTANT - R1279D COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 731-1602; COMPND 5 SYNONYM: MET-1,DNA METHYLTRANSFERASE MMUI,M.MMUI,MCMT; COMPND 6 EC: 2.1.1.37; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DNMT1, DNMT, MET1, UIM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS MUTANT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.YE,S.J.CHEN REVDAT 3 08-NOV-23 5GUV 1 REMARK REVDAT 2 13-MAR-19 5GUV 1 JRNL REVDAT 1 30-AUG-17 5GUV 0 JRNL AUTH F.YE,X.Q.KONG,H.ZHANG,Y.LIU,Z.SHAO,J.JIN,Y.CAI,R.ZHANG,L.LI, JRNL AUTH 2 Y.W.ZHANG,Y.C.LIU,C.ZHANG,W.XIE,K.YU,H.DING,K.ZHAO,S.CHEN, JRNL AUTH 3 H.JIANG,S.B.BAYLIN,C.LUO JRNL TITL BIOCHEMICAL STUDIES AND MOLECULAR DYNAMIC SIMULATIONS REVEAL JRNL TITL 2 THE MOLECULAR BASIS OF CONFORMATIONAL CHANGES IN DNA JRNL TITL 3 METHYLTRANSFERASE-1. JRNL REF ACS CHEM. BIOL. V. 13 772 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 29381856 JRNL DOI 10.1021/ACSCHEMBIO.7B00890 REMARK 2 REMARK 2 RESOLUTION. 3.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 24047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1233 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 61.6139 - 6.4008 0.97 2748 142 0.2049 0.2471 REMARK 3 2 6.4008 - 5.0813 0.99 2569 146 0.2099 0.2502 REMARK 3 3 5.0813 - 4.4392 0.99 2535 135 0.1860 0.2059 REMARK 3 4 4.4392 - 4.0334 0.99 2510 155 0.1982 0.2636 REMARK 3 5 4.0334 - 3.7444 0.99 2507 119 0.2187 0.2630 REMARK 3 6 3.7444 - 3.5236 0.99 2494 143 0.2281 0.3596 REMARK 3 7 3.5236 - 3.3472 0.99 2492 138 0.2377 0.2764 REMARK 3 8 3.3472 - 3.2015 0.99 2484 122 0.2443 0.3064 REMARK 3 9 3.2015 - 3.0782 0.99 2475 133 0.2541 0.3350 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.900 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 : 0.013 6652 REMARK 3 ANGLE : 1.804 9029 REMARK 3 CHIRALITY : 0.101 954 REMARK 3 PLANARITY : 0.011 1187 REMARK 3 DIHEDRAL : 20.317 2450 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5GUV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001366. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24332 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.078 REMARK 200 RESOLUTION RANGE LOW (A) : 61.602 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 27.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 3PT9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 1500, 100MM SPG, PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 196.63800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.51950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.51950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 98.31900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.51950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.51950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 294.95700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.51950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.51950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 98.31900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.51950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.51950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 294.95700 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 196.63800 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 LYS A 731 REMARK 465 ASP A 732 REMARK 465 GLY A 851 REMARK 465 THR A 852 REMARK 465 ASP A 853 REMARK 465 PRO A 854 REMARK 465 GLU A 855 REMARK 465 THR A 856 REMARK 465 THR A 857 REMARK 465 LEU A 858 REMARK 465 PRO A 859 REMARK 465 GLY A 860 REMARK 465 ALA A 861 REMARK 465 GLU A 862 REMARK 465 ASP A 863 REMARK 465 GLY A 864 REMARK 465 LYS A 865 REMARK 465 SER A 981 REMARK 465 ASP A 982 REMARK 465 TYR A 983 REMARK 465 ILE A 984 REMARK 465 LYS A 985 REMARK 465 GLY A 986 REMARK 465 SER A 987 REMARK 465 ASN A 988 REMARK 465 GLY A 1110 REMARK 465 ASN A 1111 REMARK 465 LYS A 1112 REMARK 465 GLY A 1113 REMARK 465 LYS A 1114 REMARK 465 GLY A 1115 REMARK 465 LYS A 1116 REMARK 465 GLY A 1117 REMARK 465 LYS A 1118 REMARK 465 GLY A 1119 REMARK 465 LYS A 1120 REMARK 465 GLY A 1121 REMARK 465 LYS A 1122 REMARK 465 GLY A 1123 REMARK 465 LYS A 1124 REMARK 465 HIS A 1125 REMARK 465 GLN A 1126 REMARK 465 VAL A 1127 REMARK 465 SER A 1128 REMARK 465 GLU A 1129 REMARK 465 PRO A 1130 REMARK 465 LYS A 1131 REMARK 465 GLU A 1132 REMARK 465 PRO A 1133 REMARK 465 GLU A 1134 REMARK 465 ALA A 1135 REMARK 465 ALA A 1136 REMARK 465 SER A 1601 REMARK 465 ALA A 1602 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 SER A 735 OG REMARK 470 SER A 773 OG REMARK 470 GLU A 844 CG CD OE1 OE2 REMARK 470 ASN A 845 CG OD1 ND2 REMARK 470 LYS A 885 CG CD CE NZ REMARK 470 GLU A 890 CG CD OE1 OE2 REMARK 470 LYS A 893 CG CD CE NZ REMARK 470 LEU A 903 CG CD1 CD2 REMARK 470 VAL A 960 CG1 CG2 REMARK 470 LYS A 961 CG CD CE NZ REMARK 470 LYS A 964 CG CD CE NZ REMARK 470 LYS A 965 CG CD CE NZ REMARK 470 ASP A 966 CG OD1 OD2 REMARK 470 LEU A 989 CG CD1 CD2 REMARK 470 LYS A1008 CG CD CE NZ REMARK 470 LYS A1009 CG CD CE NZ REMARK 470 LYS A1011 CG CD CE NZ REMARK 470 LEU A1072 CG CD1 CD2 REMARK 470 GLN A1076 CG CD OE1 NE2 REMARK 470 GLN A1080 CG CD OE1 NE2 REMARK 470 ILE A1137 CG1 CG2 CD1 REMARK 470 LYS A1138 CG CD CE NZ REMARK 470 ARG A1340 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1351 CG CD CE NZ REMARK 470 SER A1397 OG REMARK 470 SER A1495 OG REMARK 470 SER A1600 OG 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 OE1 GLU A 881 O HOH A 1801 1.86 REMARK 500 OG SER A 1480 O ALA A 1486 2.09 REMARK 500 OD1 ASP A 1414 NH1 ARG A 1574 2.13 REMARK 500 OE1 GLU A 1014 O HOH A 1802 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A1073 CG GLU A1073 CD 0.107 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 MET A 848 CA - CB - CG ANGL. DEV. = -11.1 DEGREES REMARK 500 GLU A1073 CA - CB - CG ANGL. DEV. = 13.3 DEGREES REMARK 500 LEU A1139 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 PRO A1228 CA - C - N ANGL. DEV. = -16.2 DEGREES REMARK 500 PRO A1228 O - C - N ANGL. DEV. = 12.0 DEGREES REMARK 500 CYS A1229 C - N - CA ANGL. DEV. = -19.8 DEGREES REMARK 500 ARG A1237 CA - C - N ANGL. DEV. = -15.6 DEGREES REMARK 500 ARG A1237 O - C - N ANGL. DEV. = 12.5 DEGREES REMARK 500 PHE A1238 C - N - CA ANGL. DEV. = -17.1 DEGREES REMARK 500 PHE A1238 CB - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 GLU A1483 N - CA - C ANGL. DEV. = 16.7 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 GLU A 744 -162.33 -114.62 REMARK 500 ASN A 845 40.94 -107.50 REMARK 500 ILE A 918 -73.58 -106.53 REMARK 500 VAL A 960 -5.62 -55.33 REMARK 500 LYS A 961 -146.52 50.75 REMARK 500 PRO A 963 175.82 -59.38 REMARK 500 LYS A 965 -160.80 61.53 REMARK 500 ASP A 966 -167.44 -129.09 REMARK 500 LYS A 979 30.20 -91.71 REMARK 500 PRO A 992 -177.98 -61.66 REMARK 500 THR A1030 -174.54 -69.86 REMARK 500 SER A1033 -148.65 52.09 REMARK 500 LYS A1097 26.56 44.44 REMARK 500 ASN A1239 -158.13 -136.38 REMARK 500 ASP A1350 -11.47 71.16 REMARK 500 SER A1361 -84.80 -134.39 REMARK 500 SER A1362 -168.34 -76.65 REMARK 500 MET A1374 29.15 -154.25 REMARK 500 GLU A1394 162.43 -46.92 REMARK 500 ASP A1438 -155.98 -148.39 REMARK 500 LYS A1485 -110.89 -117.25 REMARK 500 ARG A1492 125.55 -39.51 REMARK 500 LEU A1599 -164.14 -114.94 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 TYR A 1408 GLN A 1409 145.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 833 10.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1859 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A1860 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A1861 DISTANCE = 6.67 ANGSTROMS 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 A1702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 796 NE2 REMARK 620 2 CYS A 823 SG 109.3 REMARK 620 3 CYS A 897 SG 117.2 115.7 REMARK 620 4 CYS A 900 SG 94.0 111.2 107.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1479 SG REMARK 620 2 CYS A1481 SG 121.3 REMARK 620 3 CYS A1487 SG 110.0 109.1 REMARK 620 4 HIS A1504 NE2 123.2 99.9 88.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GUT RELATED DB: PDB DBREF 5GUV A 731 1602 UNP P13864 DNMT1_MOUSE 731 1602 SEQADV 5GUV ASP A 1279 UNP P13864 ARG 1279 ENGINEERED MUTATION SEQRES 1 A 872 LYS ASP ARG ILE SER TRP LEU GLY GLN PRO MET LYS ILE SEQRES 2 A 872 GLU GLU ASN ARG THR TYR TYR GLN LYS VAL SER ILE ASP SEQRES 3 A 872 GLU GLU MET LEU GLU VAL GLY ASP CYS VAL SER VAL ILE SEQRES 4 A 872 PRO ASP ASP SER SER LYS PRO LEU TYR LEU ALA ARG VAL SEQRES 5 A 872 THR ALA LEU TRP GLU ASP LYS ASN GLY GLN MET MET PHE SEQRES 6 A 872 HIS ALA HIS TRP PHE CYS ALA GLY THR ASP THR VAL LEU SEQRES 7 A 872 GLY ALA THR SER ASP PRO LEU GLU LEU PHE LEU VAL GLY SEQRES 8 A 872 GLU CYS GLU ASN MET GLN LEU SER TYR ILE HIS SER LYS SEQRES 9 A 872 VAL LYS VAL ILE TYR LYS ALA PRO SER GLU ASN TRP ALA SEQRES 10 A 872 MET GLU GLY GLY THR ASP PRO GLU THR THR LEU PRO GLY SEQRES 11 A 872 ALA GLU ASP GLY LYS THR TYR PHE PHE GLN LEU TRP TYR SEQRES 12 A 872 ASN GLN GLU TYR ALA ARG PHE GLU SER PRO PRO LYS THR SEQRES 13 A 872 GLN PRO THR GLU ASP ASN LYS HIS LYS PHE CYS LEU SER SEQRES 14 A 872 CYS ILE ARG LEU ALA GLU LEU ARG GLN LYS GLU MET PRO SEQRES 15 A 872 LYS VAL LEU GLU GLN ILE GLU GLU VAL ASP GLY ARG VAL SEQRES 16 A 872 TYR CYS SER SER ILE THR LYS ASN GLY VAL VAL TYR ARG SEQRES 17 A 872 LEU GLY ASP SER VAL TYR LEU PRO PRO GLU ALA PHE THR SEQRES 18 A 872 PHE ASN ILE LYS VAL ALA SER PRO VAL LYS ARG PRO LYS SEQRES 19 A 872 LYS ASP PRO VAL ASN GLU THR LEU TYR PRO GLU HIS TYR SEQRES 20 A 872 ARG LYS TYR SER ASP TYR ILE LYS GLY SER ASN LEU ASP SEQRES 21 A 872 ALA PRO GLU PRO TYR ARG ILE GLY ARG ILE LYS GLU ILE SEQRES 22 A 872 HIS CYS GLY LYS LYS LYS GLY LYS VAL ASN GLU ALA ASP SEQRES 23 A 872 ILE LYS LEU ARG LEU TYR LYS PHE TYR ARG PRO GLU ASN SEQRES 24 A 872 THR HIS ARG SER TYR ASN GLY SER TYR HIS THR ASP ILE SEQRES 25 A 872 ASN MET LEU TYR TRP SER ASP GLU GLU ALA VAL VAL ASN SEQRES 26 A 872 PHE SER ASP VAL GLN GLY ARG CYS THR VAL GLU TYR GLY SEQRES 27 A 872 GLU ASP LEU LEU GLU SER ILE GLN ASP TYR SER GLN GLY SEQRES 28 A 872 GLY PRO ASP ARG PHE TYR PHE LEU GLU ALA TYR ASN SER SEQRES 29 A 872 LYS THR LYS ASN PHE GLU ASP PRO PRO ASN HIS ALA ARG SEQRES 30 A 872 SER PRO GLY ASN LYS GLY LYS GLY LYS GLY LYS GLY LYS SEQRES 31 A 872 GLY LYS GLY LYS HIS GLN VAL SER GLU PRO LYS GLU PRO SEQRES 32 A 872 GLU ALA ALA ILE LYS LEU PRO LYS LEU ARG THR LEU ASP SEQRES 33 A 872 VAL PHE SER GLY CYS GLY GLY LEU SER GLU GLY PHE HIS SEQRES 34 A 872 GLN ALA GLY ILE SER GLU THR LEU TRP ALA ILE GLU MET SEQRES 35 A 872 TRP ASP PRO ALA ALA GLN ALA PHE ARG LEU ASN ASN PRO SEQRES 36 A 872 GLY THR THR VAL PHE THR GLU ASP CYS ASN VAL LEU LEU SEQRES 37 A 872 LYS LEU VAL MET ALA GLY GLU VAL THR ASN SER LEU GLY SEQRES 38 A 872 GLN ARG LEU PRO GLN LYS GLY ASP VAL GLU MET LEU CYS SEQRES 39 A 872 GLY GLY PRO PRO CYS GLN GLY PHE SER GLY MET ASN ARG SEQRES 40 A 872 PHE ASN SER ARG THR TYR SER LYS PHE LYS ASN SER LEU SEQRES 41 A 872 VAL VAL SER PHE LEU SER TYR CYS ASP TYR TYR ARG PRO SEQRES 42 A 872 ARG PHE PHE LEU LEU GLU ASN VAL ARG ASN PHE VAL SER SEQRES 43 A 872 TYR ARG ASP SER MET VAL LEU LYS LEU THR LEU ARG CYS SEQRES 44 A 872 LEU VAL ARG MET GLY TYR GLN CYS THR PHE GLY VAL LEU SEQRES 45 A 872 GLN ALA GLY GLN TYR GLY VAL ALA GLN THR ARG ARG ARG SEQRES 46 A 872 ALA ILE ILE LEU ALA ALA ALA PRO GLY GLU LYS LEU PRO SEQRES 47 A 872 LEU PHE PRO GLU PRO LEU HIS VAL PHE ALA PRO ARG ALA SEQRES 48 A 872 CYS GLN LEU SER VAL VAL VAL ASP ASP LYS LYS PHE VAL SEQRES 49 A 872 SER ASN ILE THR ARG LEU SER SER GLY PRO PHE ARG THR SEQRES 50 A 872 ILE THR VAL ARG ASP THR MET SER ASP LEU PRO GLU ILE SEQRES 51 A 872 GLN ASN GLY ALA SER ASN SER GLU ILE PRO TYR ASN GLY SEQRES 52 A 872 GLU PRO LEU SER TRP PHE GLN ARG GLN LEU ARG GLY SER SEQRES 53 A 872 HIS TYR GLN PRO ILE LEU ARG ASP HIS ILE CYS LYS ASP SEQRES 54 A 872 MET SER PRO LEU VAL ALA ALA ARG MET ARG HIS ILE PRO SEQRES 55 A 872 LEU PHE PRO GLY SER ASP TRP ARG ASP LEU PRO ASN ILE SEQRES 56 A 872 GLN VAL ARG LEU GLY ASP GLY VAL ILE ALA HIS LYS LEU SEQRES 57 A 872 GLN TYR THR PHE HIS ASP VAL LYS ASN GLY TYR SER SER SEQRES 58 A 872 THR GLY ALA LEU ARG GLY VAL CYS SER CYS ALA GLU GLY SEQRES 59 A 872 LYS ALA CYS ASP PRO GLU SER ARG GLN PHE SER THR LEU SEQRES 60 A 872 ILE PRO TRP CYS LEU PRO HIS THR GLY ASN ARG HIS ASN SEQRES 61 A 872 HIS TRP ALA GLY LEU TYR GLY ARG LEU GLU TRP ASP GLY SEQRES 62 A 872 PHE PHE SER THR THR VAL THR ASN PRO GLU PRO MET GLY SEQRES 63 A 872 LYS GLN GLY ARG VAL LEU HIS PRO GLU GLN HIS ARG VAL SEQRES 64 A 872 VAL SER VAL ARG GLU CYS ALA ARG SER GLN GLY PHE PRO SEQRES 65 A 872 ASP SER TYR ARG PHE PHE GLY ASN ILE LEU ASP ARG HIS SEQRES 66 A 872 ARG GLN VAL GLY ASN ALA VAL PRO PRO PRO LEU ALA LYS SEQRES 67 A 872 ALA ILE GLY LEU GLU ILE LYS LEU CYS LEU LEU SER SER SEQRES 68 A 872 ALA HET ZN A1701 1 HET ZN A1702 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *61(H2 O) HELIX 1 AA1 THR A 804 THR A 806 5 3 HELIX 2 AA2 LEU A 808 SER A 812 5 5 HELIX 3 AA3 SER A 829 ILE A 831 5 3 HELIX 4 AA4 ASN A 845 GLU A 849 5 5 HELIX 5 AA5 CYS A 897 MET A 911 1 15 HELIX 6 AA6 GLU A 975 LYS A 979 5 5 HELIX 7 AA7 ARG A 1026 THR A 1030 5 5 HELIX 8 AA8 SER A 1057 VAL A 1059 5 3 HELIX 9 AA9 GLU A 1069 LEU A 1071 5 3 HELIX 10 AB1 SER A 1074 GLY A 1082 1 9 HELIX 11 AB2 PRO A 1103 ARG A 1107 5 5 HELIX 12 AB3 GLY A 1152 GLY A 1162 1 11 HELIX 13 AB4 TRP A 1173 ASN A 1184 1 12 HELIX 14 AB5 ASP A 1193 ALA A 1203 1 11 HELIX 15 AB6 ASN A 1239 ASN A 1248 1 10 HELIX 16 AB7 SER A 1249 ARG A 1262 1 14 HELIX 17 AB8 ASN A 1273 VAL A 1275 5 3 HELIX 18 AB9 SER A 1276 GLY A 1294 1 19 HELIX 19 AC1 GLY A 1305 GLY A 1308 5 4 HELIX 20 AC2 ALA A 1338 CYS A 1342 5 5 HELIX 21 AC3 THR A 1369 SER A 1375 1 7 HELIX 22 AC4 SER A 1397 GLY A 1405 1 9 HELIX 23 AC5 SER A 1421 HIS A 1430 1 10 HELIX 24 AC6 ASP A 1438 LEU A 1442 5 5 HELIX 25 AC7 CYS A 1479 GLY A 1484 5 6 HELIX 26 AC8 TRP A 1500 GLY A 1506 1 7 HELIX 27 AC9 ASN A 1507 ALA A 1513 5 7 HELIX 28 AD1 SER A 1551 GLN A 1559 1 9 HELIX 29 AD2 ASN A 1570 ALA A 1581 1 12 HELIX 30 AD3 PRO A 1583 CYS A 1597 1 15 SHEET 1 AA1 3 ILE A 734 LEU A 737 0 SHEET 2 AA1 3 LYS A 752 ILE A 755 -1 O SER A 754 N SER A 735 SHEET 3 AA1 3 GLU A 758 GLU A 761 -1 O LEU A 760 N VAL A 753 SHEET 1 AA2 7 LYS A 742 ILE A 743 0 SHEET 2 AA2 7 ARG A 747 TYR A 749 -1 O TYR A 749 N LYS A 742 SHEET 3 AA2 7 TRP A 786 ASP A 788 -1 O GLU A 787 N THR A 748 SHEET 4 AA2 7 MET A 793 ALA A 802 -1 O MET A 794 N TRP A 786 SHEET 5 AA2 7 GLU A 816 GLN A 827 -1 O PHE A 818 N CYS A 801 SHEET 6 AA2 7 TYR A 867 ASN A 874 1 O TYR A 873 N LEU A 819 SHEET 7 AA2 7 VAL A 837 TYR A 839 1 N ILE A 838 O PHE A 869 SHEET 1 AA314 SER A 833 VAL A 835 0 SHEET 2 AA314 CYS A 765 VAL A 768 -1 N CYS A 765 O VAL A 835 SHEET 3 AA314 TYR A 778 VAL A 782 -1 O ALA A 780 N VAL A 766 SHEET 4 AA314 MET A 793 ALA A 802 -1 O PHE A 800 N LEU A 779 SHEET 5 AA314 GLU A 816 GLN A 827 -1 O PHE A 818 N CYS A 801 SHEET 6 AA314 TYR A 867 ASN A 874 1 O TYR A 873 N LEU A 819 SHEET 7 AA314 ARG A 879 GLU A 881 -1 O GLU A 881 N TRP A 872 SHEET 8 AA314 GLN A1296 GLN A1303 -1 O CYS A1297 N PHE A 880 SHEET 9 AA314 ARG A1314 ALA A1321 -1 O ALA A1321 N GLN A1296 SHEET 10 AA314 PHE A1265 VAL A1271 -1 N LEU A1268 O ILE A1318 SHEET 11 AA314 MET A1222 GLY A1225 1 N GLY A1225 O GLU A1269 SHEET 12 AA314 LEU A1142 VAL A1147 1 N LEU A1145 O MET A1222 SHEET 13 AA314 SER A1164 ILE A1170 1 O GLU A1165 N THR A1144 SHEET 14 AA314 THR A1188 PHE A1190 1 O PHE A1190 N ALA A1169 SHEET 1 AA4 7 LYS A 913 GLU A 920 0 SHEET 2 AA4 7 VAL A 925 LYS A 932 -1 O TYR A 926 N ILE A 918 SHEET 3 AA4 7 ARG A 996 LYS A1008 -1 O ILE A1003 N CYS A 927 SHEET 4 AA4 7 SER A 942 LEU A 945 -1 N LEU A 945 O ARG A 996 SHEET 5 AA4 7 GLY A1061 TYR A1067 -1 O GLY A1061 N TYR A 944 SHEET 6 AA4 7 ARG A1085 ASN A1093 1 O PHE A1086 N THR A1064 SHEET 7 AA4 7 MET A1044 TRP A1047 1 N LEU A1045 O TYR A1087 SHEET 1 AA5 5 VAL A 935 ARG A 938 0 SHEET 2 AA5 5 VAL A 925 LYS A 932 -1 N ILE A 930 O TYR A 937 SHEET 3 AA5 5 ARG A 996 LYS A1008 -1 O ILE A1003 N CYS A 927 SHEET 4 AA5 5 LYS A1011 LYS A1023 -1 O LYS A1011 N LYS A1008 SHEET 5 AA5 5 GLU A1051 ASN A1055 -1 O ALA A1052 N LEU A1021 SHEET 1 AA6 7 GLU A1051 ASN A1055 0 SHEET 2 AA6 7 LYS A1011 LYS A1023 -1 N LEU A1021 O ALA A1052 SHEET 3 AA6 7 ARG A 996 LYS A1008 -1 N LYS A1008 O LYS A1011 SHEET 4 AA6 7 SER A 942 LEU A 945 -1 N LEU A 945 O ARG A 996 SHEET 5 AA6 7 GLY A1061 TYR A1067 -1 O GLY A1061 N TYR A 944 SHEET 6 AA6 7 ARG A1085 ASN A1093 1 O PHE A1086 N THR A1064 SHEET 7 AA6 7 ASN A1098 GLU A1100 -1 O GLU A1100 N ALA A1091 SHEET 1 AA7 2 VAL A1346 VAL A1348 0 SHEET 2 AA7 2 LYS A1351 PHE A1353 -1 O PHE A1353 N VAL A1346 SHEET 1 AA8 2 GLU A1388 PRO A1390 0 SHEET 2 AA8 2 ILE A1411 ARG A1413 -1 O LEU A1412 N ILE A1389 SHEET 1 AA9 2 VAL A1447 ARG A1448 0 SHEET 2 AA9 2 ILE A1454 ALA A1455 -1 O ALA A1455 N VAL A1447 LINK NE2 HIS A 796 ZN ZN A1702 1555 1555 1.95 LINK SG CYS A 823 ZN ZN A1702 1555 1555 2.18 LINK SG CYS A 897 ZN ZN A1702 1555 1555 2.23 LINK SG CYS A 900 ZN ZN A1702 1555 1555 2.12 LINK SG CYS A1479 ZN ZN A1701 1555 1555 2.29 LINK SG CYS A1481 ZN ZN A1701 1555 1555 2.15 LINK SG CYS A1487 ZN ZN A1701 1555 1555 2.93 LINK NE2 HIS A1504 ZN ZN A1701 1555 1555 2.43 CISPEP 1 GLU A 1483 GLY A 1484 0 -24.64 SITE 1 AC1 4 CYS A1479 CYS A1481 CYS A1487 HIS A1504 SITE 1 AC2 4 HIS A 796 CYS A 823 CYS A 897 CYS A 900 CRYST1 79.039 79.039 393.276 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 0.012652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002543 0.00000