HEADER TRANSFERASE 06-JAN-23 8C59 TITLE CPG SPECIFIC M.MPEI METHYLTRANSFERASE CRYSTALLIZED IN THE PRESENCE OF TITLE 2 5-BROMOCYTOSINE (CONVERTED TO 5MC) AND 5-METHYLCYTOSINE CONTAINING TITLE 3 DSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSINE-SPECIFIC METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*A)- COMPND 7 3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)- COMPND 12 3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MALACOPLASMA PENETRANS HF-2; SOURCE 3 ORGANISM_TAXID: 272633; SOURCE 4 STRAIN: HF-2; SOURCE 5 GENE: MYPE4940; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: 2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS M.MPEI, DNA METHYLTRANSFERASE, DNA, 5-METHYLCYTOSINE, 5- KEYWDS 2 BROMOCYTOSINE, 5BRC, 5MC, CPG, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.WOJCIECHOWSKI,H.CZAPINSKA,J.KRWAWICZ,D.RAFALSKI,M.BOCHTLER REVDAT 1 17-JAN-24 8C59 0 JRNL AUTH M.WOJCIECHOWSKI,H.CZAPINSKA,J.KRWAWICZ,D.RAFALSKI,M.BOCHTLER JRNL TITL CYTOSINE ANALOGUES AS DNA METHYLTRANSFERASE SUBSTRATES AND JRNL TITL 2 INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.WOJCIECHOWSKI,H.CZAPINSKA,M.BOCHTLER REMARK 1 TITL CPG UNDERREPRESENTATION AND THE BACTERIAL CPG-SPECIFIC DNA REMARK 1 TITL 2 METHYLTRANSFERASE M.MPEI. REMARK 1 REF PROC. NATL. ACAD. SCI. V. 110 105 2013 REMARK 1 REF 2 U.S.A. REMARK 1 REFN ESSN 1091-6490 REMARK 1 PMID 23248272 REMARK 1 DOI 10.1073/PNAS.1207986110 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.SONG,M.TEPLOVA,S.ISHIBE-MURAKAMI,D.J.PATEL REMARK 1 TITL STRUCTURE-BASED MECHANISTIC INSIGHTS INTO DNMT1-MEDIATED REMARK 1 TITL 2 MAINTENANCE DNA METHYLATION. REMARK 1 REF SCIENCE V. 335 709 2012 REMARK 1 REFN ESSN 1095-9203 REMARK 1 PMID 22323818 REMARK 1 DOI 10.1126/SCIENCE.1214453 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 66340 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3498 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4770 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 252 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3107 REMARK 3 NUCLEIC ACID ATOMS : 570 REMARK 3 HETEROGEN ATOMS : 99 REMARK 3 SOLVENT ATOMS : 591 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38000 REMARK 3 B22 (A**2) : 0.38000 REMARK 3 B33 (A**2) : -0.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.723 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4279 ; 0.006 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3864 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5907 ; 1.140 ; 1.864 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8994 ; 0.818 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 452 ; 5.595 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;36.653 ;25.273 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 726 ;13.037 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;14.068 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 609 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4513 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 978 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1709 ; 0.679 ; 2.268 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1709 ; 0.679 ; 2.268 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2194 ; 1.190 ; 3.390 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2195 ; 1.190 ; 3.391 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2570 ; 0.778 ; 2.510 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2565 ; 0.778 ; 2.507 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3710 ; 1.342 ; 3.723 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5704 ; 5.938 ;29.941 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5340 ; 5.083 ;27.761 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 393 REMARK 3 RESIDUE RANGE : B 1 B 7 REMARK 3 RESIDUE RANGE : C 1 C 14 REMARK 3 ORIGIN FOR THE GROUP (A): 22.7610 22.4400 46.0660 REMARK 3 T TENSOR REMARK 3 T11: 0.0387 T22: 0.1266 REMARK 3 T33: 0.0050 T12: -0.0238 REMARK 3 T13: 0.0006 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.9903 L22: 1.9251 REMARK 3 L33: 0.9666 L12: 0.8856 REMARK 3 L13: -0.0374 L23: 0.3458 REMARK 3 S TENSOR REMARK 3 S11: 0.0909 S12: -0.1558 S13: 0.0272 REMARK 3 S21: 0.0029 S22: -0.1216 S23: -0.0100 REMARK 3 S31: -0.0614 S32: 0.0753 S33: 0.0307 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: REMARK 3 HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 U VALUES : WITH TLS ADDED. REMARK 3 IONS AND SOLVENT MOLECULES HAVE BEEN MODELLED TENTATIVELY. REMARK 3 S-ADENOSYLMETHIONINE (SAM) HAS BEEN MODELLED IN THE CO-SUBSTRATE REMARK 3 BINDING POCKET BUT ONLY PARTS OF THE MOLECULE CORRESPONDING TO ITS REMARK 3 BASE AND AMINO ACID END ARE RESOLVED IN THE ELECTRON DENSITY. THE REMARK 3 CENTRAL PART OF THE CO-SUBSTRATE COULD NOT BE UNAMBIGUOUSLY TRACED, REMARK 3 WHICH MAY BE DUE TO ITS DECOMPOSITION TO HOMOSERINE LACTONE (HSL) REMARK 3 AND METHYLTHIOADENOSINE (MTA). REMARK 3 5-BROMOCYTOSINE CONTAINING DNA HAS BEEN USED FOR CRYSTALLIZATION REMARK 3 BUT 5-METHYLCYTOSINE IS OBSERVED IN THE CRYSTALS IN THE M.MPEI REMARK 3 SUBSTRATE BINDING POCKET WHICH INDICATES THAT THE REACTION MUST REMARK 3 HAVE TAKEN PLACE EITHER IN SOLUTION PRIOR TO CRYSTALLIZATION OR IN REMARK 3 THE CRYSTAL. REMARK 3 THE RESIDUAL DIFFERENCE DENSITY NEXT TO THE SUBSTRATE BASE LIKELY REMARK 3 RESULTS FROM THE RESIDUAL PRESENCE OF THE ACTIVE SITE LOOP IN THE " REMARK 3 IN" CONFORMATION BUT THE OCCUPANCY OF THIS CONFORMER WAS TOO LOW REMARK 3 TO BE INCLUDED IN THE MODEL. REMARK 3 SINCE THE PH OF THE CRYSTALLIZATION DROP (RESERVOIR BUFFER PH 5.6) REMARK 3 WAS CLOSE TO THE PK FOR THE HCO3-/CO32-+H+ EQUILIBRIUM (PKA=6.1), REMARK 3 A MIXTURE OF CARBONATE AND HYDROGENCARBONATE IS LIKELY PRESENT IN REMARK 3 THE CRYSTAL. REMARK 4 REMARK 4 8C59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1292108686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91160 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.780 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03900 REMARK 200 FOR THE DATA SET : 27.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.52 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.91900 REMARK 200 FOR SHELL : 2.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4DKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 150 MM NACL, 50 MM REMARK 280 SODIUM CITRATE (FINAL PH, 5.6). FOR CRYOPROTECTION GLYCEROL WAS REMARK 280 ADDED TO 25% V/V, PH 5.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K 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 86.55750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.25550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.25550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.27875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.25550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.25550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 129.83625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.25550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.25550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.27875 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.25550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.25550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 129.83625 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 86.55750 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 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 SER A 3 REMARK 465 ASN A 4 REMARK 465 LYS A 5 REMARK 465 ASP A 6 REMARK 465 GLY A 142 REMARK 465 LEU A 143 REMARK 465 GLN A 144 REMARK 465 LYS A 145 REMARK 465 GLY A 146 REMARK 465 ILE A 147 REMARK 465 ASP A 148 REMARK 465 LYS A 149 REMARK 465 GLU A 150 REMARK 465 LEU A 151 REMARK 465 ASN A 152 REMARK 465 GLU A 394 REMARK 465 GLU A 395 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 DT B 6 C1' - O4' - C4' ANGL. DEV. = -6.8 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 SER A 80 -11.56 87.95 REMARK 500 PHE A 112 -57.27 73.16 REMARK 500 PHE A 133 148.90 -170.56 REMARK 500 CYS A 225 32.50 -99.25 REMARK 500 ASN A 270 37.08 -142.41 REMARK 500 TYR A 299 -64.90 -93.07 REMARK 500 ARG A 326 72.44 -119.17 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 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 90 O REMARK 620 2 ASN A 93 O 89.4 REMARK 620 3 CIT A 410 O7 103.8 164.2 REMARK 620 4 CIT A 410 O6 154.4 101.3 63.1 REMARK 620 5 CIT A 410 O4 82.4 104.7 69.2 72.4 REMARK 620 6 HOH A 662 O 95.1 94.9 92.6 106.9 160.2 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DKJ RELATED DB: PDB REMARK 900 M.MPEI METHYLTRANSFERASE IN COMPLEX WITH 5FC/5MC CONTAINING TARGET REMARK 900 DNA REMARK 900 RELATED ID: 4DA4 RELATED DB: PDB REMARK 900 MOUSE DNMT1 (731-1602) BOUND TO HEMIMETHYLATED CPG DNA REMARK 900 RELATED ID: 8C56 RELATED DB: PDB REMARK 900 CPG SPECIFIC M.MPEI METHYLTRANSFERASE CRYSTALLIZED IN THE PRESENCE REMARK 900 OF 2'-DEOXY-5-METHYLZEBULARINE (5MZ) AND 5-METHYLCYTOSINE REMARK 900 CONTAINING DSDNA REMARK 900 RELATED ID: 8C57 RELATED DB: PDB REMARK 900 CPG SPECIFIC M.MPEI METHYLTRANSFERASE CRYSTALLIZED IN THE PRESENCE REMARK 900 OF 5,6-DIHYDRO-5-AZACYTOSINE (CONVERTED TO 5M-DHAC) AND 5- REMARK 900 METHYLCYTOSINE CONTAINING DSDNA REMARK 900 RELATED ID: 8C58 RELATED DB: PDB REMARK 900 CPG SPECIFIC M.MPEI METHYLTRANSFERASE CRYSTALLIZED IN THE PRESENCE REMARK 900 OF 5-HYDROXYCYTOSINE AND 5-METHYLCYTOSINE CONTAINING DSDNA DBREF 8C59 A 1 395 UNP Q8EVR5 Q8EVR5_MALP2 1 395 DBREF 8C59 B 1 14 PDB 8C59 8C59 1 14 DBREF 8C59 C 1 14 PDB 8C59 8C59 1 14 SEQADV 8C59 ARG A 68 UNP Q8EVR5 GLN 68 CLONING ARTIFACT SEQADV 8C59 ARG A 71 UNP Q8EVR5 LYS 71 CLONING ARTIFACT SEQADV 8C59 PRO A 295 UNP Q8EVR5 SER 295 CLONING ARTIFACT SEQRES 1 A 395 MET ASN SER ASN LYS ASP LYS ILE LYS VAL ILE LYS VAL SEQRES 2 A 395 PHE GLU ALA PHE ALA GLY ILE GLY SER GLN PHE LYS ALA SEQRES 3 A 395 LEU LYS ASN ILE ALA ARG SER LYS ASN TRP GLU ILE GLN SEQRES 4 A 395 HIS SER GLY MET VAL GLU TRP PHE VAL ASP ALA ILE VAL SEQRES 5 A 395 SER TYR VAL ALA ILE HIS SER LYS ASN PHE ASN PRO LYS SEQRES 6 A 395 ILE GLU ARG LEU ASP ARG ASP ILE LEU SER ILE SER ASN SEQRES 7 A 395 ASP SER LYS MET PRO ILE SER GLU TYR GLY ILE LYS LYS SEQRES 8 A 395 ILE ASN ASN THR ILE LYS ALA SER TYR LEU ASN TYR ALA SEQRES 9 A 395 LYS LYS HIS PHE ASN ASN LEU PHE ASP ILE LYS LYS VAL SEQRES 10 A 395 ASN LYS ASP ASN PHE PRO LYS ASN ILE ASP ILE PHE THR SEQRES 11 A 395 TYR SER PHE PRO CYS GLN ASP LEU SER VAL GLN GLY LEU SEQRES 12 A 395 GLN LYS GLY ILE ASP LYS GLU LEU ASN THR ARG SER GLY SEQRES 13 A 395 LEU LEU TRP GLU ILE GLU ARG ILE LEU GLU GLU ILE LYS SEQRES 14 A 395 ASN SER PHE SER LYS GLU GLU MET PRO LYS TYR LEU LEU SEQRES 15 A 395 MET GLU ASN VAL LYS ASN LEU LEU SER HIS LYS ASN LYS SEQRES 16 A 395 LYS ASN TYR ASN THR TRP LEU LYS GLN LEU GLU LYS PHE SEQRES 17 A 395 GLY TYR LYS SER LYS THR TYR LEU LEU ASN SER LYS ASN SEQRES 18 A 395 PHE ASP ASN CYS GLN ASN ARG GLU ARG VAL PHE CYS LEU SEQRES 19 A 395 SER ILE ARG ASP ASP TYR LEU GLU LYS THR GLY PHE LYS SEQRES 20 A 395 PHE LYS GLU LEU GLU LYS VAL LYS ASN PRO PRO LYS LYS SEQRES 21 A 395 ILE LYS ASP ILE LEU VAL ASP SER SER ASN TYR LYS TYR SEQRES 22 A 395 LEU ASN LEU ASN LYS TYR GLU THR THR THR PHE ARG GLU SEQRES 23 A 395 THR LYS SER ASN ILE ILE SER ARG PRO LEU LYS ASN TYR SEQRES 24 A 395 THR THR PHE ASN SER GLU ASN TYR VAL TYR ASN ILE ASN SEQRES 25 A 395 GLY ILE GLY PRO THR LEU THR ALA SER GLY ALA ASN SER SEQRES 26 A 395 ARG ILE LYS ILE GLU THR GLN GLN GLY VAL ARG TYR LEU SEQRES 27 A 395 THR PRO LEU GLU CYS PHE LYS TYR MET GLN PHE ASP VAL SEQRES 28 A 395 ASN ASP PHE LYS LYS VAL GLN SER THR ASN LEU ILE SER SEQRES 29 A 395 GLU ASN LYS MET ILE TYR ILE ALA GLY ASN SER ILE PRO SEQRES 30 A 395 VAL LYS ILE LEU GLU ALA ILE PHE ASN THR LEU GLU PHE SEQRES 31 A 395 VAL ASN ASN GLU GLU SEQRES 1 B 14 DC DC DA DC DA DT DG 5CM DG DC DT DG DA SEQRES 2 B 14 DA SEQRES 1 C 14 DG DT DT DC DA DG 5CM DG DC DA DT DG DT SEQRES 2 C 14 DG HET 5CM B 8 20 HET 5CM C 7 20 HET SAM A 401 27 HET NA A 402 1 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HET GOL A 407 6 HET GOL A 408 6 HET GOL A 409 6 HET CIT A 410 13 HET GOL B 101 6 HET GOL C 101 6 HET CO3 C 102 4 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAM S-ADENOSYLMETHIONINE HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM CIT CITRIC ACID HETNAM CO3 CARBONATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 4 SAM C15 H22 N6 O5 S FORMUL 5 NA NA 1+ FORMUL 6 GOL 9(C3 H8 O3) FORMUL 13 CIT C6 H8 O7 FORMUL 16 CO3 C O3 2- FORMUL 17 HOH *591(H2 O) HELIX 1 AA1 GLY A 21 ASN A 35 1 15 HELIX 2 AA2 PHE A 47 SER A 59 1 13 HELIX 3 AA3 SER A 85 ASN A 93 1 9 HELIX 4 AA4 THR A 95 ASN A 109 1 15 HELIX 5 AA5 ASP A 113 VAL A 117 5 5 HELIX 6 AA6 PRO A 134 SER A 139 5 6 HELIX 7 AA7 SER A 155 PHE A 172 1 18 HELIX 8 AA8 SER A 173 MET A 177 5 5 HELIX 9 AA9 ASN A 188 SER A 191 5 4 HELIX 10 AB1 ASN A 194 PHE A 208 1 15 HELIX 11 AB2 LYS A 220 PHE A 222 5 3 HELIX 12 AB3 ASP A 238 GLY A 245 1 8 HELIX 13 AB4 GLU A 250 VAL A 254 5 5 HELIX 14 AB5 LYS A 260 ILE A 264 5 5 HELIX 15 AB6 PHE A 302 GLU A 305 5 4 HELIX 16 AB7 GLY A 322 ARG A 326 5 5 HELIX 17 AB8 THR A 339 MET A 347 1 9 HELIX 18 AB9 ASP A 350 THR A 360 1 11 HELIX 19 AC1 SER A 364 ASN A 374 1 11 HELIX 20 AC2 PRO A 377 ASN A 386 1 10 SHEET 1 AA1 6 TRP A 36 VAL A 44 0 SHEET 2 AA1 6 LYS A 9 ALA A 16 1 N ILE A 11 O GLN A 39 SHEET 3 AA1 6 ILE A 128 TYR A 131 1 O ILE A 128 N PHE A 14 SHEET 4 AA1 6 TYR A 180 VAL A 186 1 O LEU A 182 N TYR A 131 SHEET 5 AA1 6 GLU A 229 ARG A 237 -1 O SER A 235 N LEU A 181 SHEET 6 AA1 6 TYR A 210 ASN A 218 -1 N TYR A 215 O PHE A 232 SHEET 1 AA2 5 ARG A 285 GLU A 286 0 SHEET 2 AA2 5 ILE A 292 PRO A 295 -1 O SER A 293 N ARG A 285 SHEET 3 AA2 5 TYR A 307 ASN A 310 -1 O ASN A 310 N ILE A 292 SHEET 4 AA2 5 LYS A 328 THR A 331 1 O LYS A 328 N TYR A 309 SHEET 5 AA2 5 GLY A 334 TYR A 337 -1 O ARG A 336 N ILE A 329 LINK O3' DG B 7 P 5CM B 8 1555 1555 1.61 LINK O3' 5CM B 8 P DG B 9 1555 1555 1.60 LINK O3' DG C 6 P 5CM C 7 1555 1555 1.60 LINK O3' 5CM C 7 P DG C 8 1555 1555 1.60 LINK O LYS A 90 NA NA A 402 1555 1555 2.40 LINK O ASN A 93 NA NA A 402 1555 1555 2.37 LINK NA NA A 402 O7 ACIT A 410 1555 1555 2.42 LINK NA NA A 402 O6 ACIT A 410 1555 1555 2.49 LINK NA NA A 402 O4 ACIT A 410 1555 1555 2.63 LINK NA NA A 402 O HOH A 662 1555 1555 2.16 CRYST1 84.511 84.511 173.115 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 0.011833 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011833 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005777 0.00000