HEADER TRANSFERASE/DNA 03-FEB-12 4DKJ TITLE CPG SPECIFIC METHYLTRANSFERASE IN COMPLEX WITH TARGET DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSINE-SPECIFIC METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.37; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP*A)- COMPND 9 3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)- COMPND 14 3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA PENETRANS; 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: ER2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS CG-SPECIFICITY, DNA INTERCALATION, CPG SEQUENCE, CYTOSINE C5- KEYWDS 2 METHYLATION, C5-METHYLCYTOSINE, NUCLEOTIDE FLIPPING, S-ADENOSYL-L- KEYWDS 3 METHIONINE-DEPENDENT METHYLTRANSFERASES, C-5 CYTOSINE-SPECIFIC DNA KEYWDS 4 METHYLASES, DNA (CYTOSINE-5-)-METHYLTRANSFERASE ACTIVITY, DNA KEYWDS 5 BINDING, DNA (CYTOSINE-5-)-METHYLATION, INTRACELLULAR, TRANSFERASE- KEYWDS 6 DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.WOJCIECHOWSKI,H.CZAPINSKA,M.BOCHTLER REVDAT 5 13-SEP-23 4DKJ 1 REMARK SEQADV LINK REVDAT 4 16-JAN-13 4DKJ 1 JRNL REVDAT 3 02-JAN-13 4DKJ 1 JRNL REVDAT 2 19-DEC-12 4DKJ 1 JRNL REVDAT 1 05-DEC-12 4DKJ 0 JRNL AUTH M.WOJCIECHOWSKI,H.CZAPINSKA,M.BOCHTLER JRNL TITL CPG UNDERREPRESENTATION AND THE BACTERIAL CPG-SPECIFIC DNA JRNL TITL 2 METHYLTRANSFERASE M.MPEI. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 105 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23248272 JRNL DOI 10.1073/PNAS.1207986110 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 34274 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1729 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2348 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3199 REMARK 3 NUCLEIC ACID ATOMS : 570 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.40 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.214 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.176 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4388 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2941 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6064 ; 1.253 ; 2.131 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7256 ; 3.966 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 471 ; 6.160 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;38.254 ;25.301 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 767 ;15.063 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.209 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4548 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 810 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 771 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2985 ; 0.232 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2059 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1868 ; 0.108 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 258 ; 0.137 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.079 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 15 ; 0.380 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.084 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 259 REMARK 3 RESIDUE RANGE : A 376 A 393 REMARK 3 ORIGIN FOR THE GROUP (A): 25.8750 30.8230 49.2440 REMARK 3 T TENSOR REMARK 3 T11: -0.0916 T22: -0.0382 REMARK 3 T33: -0.0857 T12: -0.0668 REMARK 3 T13: 0.0118 T23: -0.0230 REMARK 3 L TENSOR REMARK 3 L11: 1.3285 L22: 1.8304 REMARK 3 L33: 1.4460 L12: 0.7139 REMARK 3 L13: 0.0899 L23: 0.2160 REMARK 3 S TENSOR REMARK 3 S11: 0.1138 S12: -0.2095 S13: 0.1597 REMARK 3 S21: 0.0245 S22: -0.0982 S23: 0.0650 REMARK 3 S31: -0.1703 S32: 0.1231 S33: -0.0156 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 260 A 375 REMARK 3 ORIGIN FOR THE GROUP (A): 12.6010 9.2560 40.5430 REMARK 3 T TENSOR REMARK 3 T11: -0.0695 T22: -0.0185 REMARK 3 T33: -0.0260 T12: -0.0421 REMARK 3 T13: -0.0339 T23: 0.0294 REMARK 3 L TENSOR REMARK 3 L11: 0.9724 L22: 2.2069 REMARK 3 L33: 0.7196 L12: 0.6691 REMARK 3 L13: -0.1999 L23: 0.0468 REMARK 3 S TENSOR REMARK 3 S11: -0.0188 S12: -0.0366 S13: -0.0063 REMARK 3 S21: -0.1209 S22: -0.0562 S23: 0.1295 REMARK 3 S31: 0.0652 S32: -0.0767 S33: 0.0749 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 14 REMARK 3 RESIDUE RANGE : C 1 C 14 REMARK 3 ORIGIN FOR THE GROUP (A): 29.0600 5.7600 43.5620 REMARK 3 T TENSOR REMARK 3 T11: -0.0503 T22: 0.0055 REMARK 3 T33: -0.0227 T12: 0.0155 REMARK 3 T13: 0.0014 T23: 0.0614 REMARK 3 L TENSOR REMARK 3 L11: 1.3002 L22: 1.9057 REMARK 3 L33: 2.1045 L12: -0.0789 REMARK 3 L13: 0.4393 L23: -0.0269 REMARK 3 S TENSOR REMARK 3 S11: 0.1105 S12: -0.0305 S13: -0.0781 REMARK 3 S21: -0.0129 S22: 0.0146 S23: -0.2426 REMARK 3 S31: 0.1346 S32: 0.3025 S33: -0.1251 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: (1) THE CRYSTAL WAS GROWN IN THE REMARK 3 PRESENCE OF A SAMPLE THAT WAS LABELLED AS S-ADENOSYL-METHIONINE REMARK 3 (SAM), BUT APPEARS TO HAVE BEEN DEGRADED TO S-ADENOSYL- REMARK 3 HOMOCYSTEINE (SAH) EITHER PRIOR TO OR DURING CRYSTALLIZATION. REMARK 3 PROGRAM CNS HAS BEEN USED FOR DNA REFINEMENT. NO SUGAR PUCKER REMARK 3 CONSTRAINTS HAVE BEEN APPLIED. (2) THE MODELLED S- REMARK 3 ADENOSYLHOMOCYSTEINE (SAH) IS UNCERTAIN. ITS BINDING SITE MIGHT REMARK 3 BE OCCUPIED IN PART BY S-ADENOSYLMETHIONINE (SAM) OR THE SAM REMARK 3 DEGRADATION PRODUCT 5 -METHYLTHIOADENOSINE (MTA) (FROM SCISSION REMARK 3 OF SAM TO MTA AND HOMOSERINE LACTONE). THE DISTANCE BETWEEN REMARK 3 CYS135 S AND C6 OF THE SUBSTRATE CYTOSINE BASE IS INTERMEDIATE REMARK 3 BETWEEN A NON-COVALENT AND A COVALENT BOND. A DISTANCE BELOW THE REMARK 3 VAN DER WAALS LIMIT SUGGESTS THAT SLIGHT DEVIATIONS FROM THE REMARK 3 PLANARITY OF THE DNA BASE SHOULD OCCUR. AS THE RESOLUTION OF THE REMARK 3 X-RAY DATA IS INSUFFICIENT TO DETECT SUCH DEVIATIONS, THEY WERE REMARK 3 NOT MODELLED. (3) HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. TLS REFINEMENT HAS BEEN USED. REMARK 4 REMARK 4 4DKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : BENT MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34324 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : 0.31000 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, CHAINSAW, REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2C7P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 150 MM NACL, 50 MM REMARK 280 SODIUM. FOR CRYOPROTECTION GLYCEROL WAS ADDED TO 25% V/V, PH 5.6, REMARK 280 VAPOR DIFFUSION, SITTING DROP, 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 86.92000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.97500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.97500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.46000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.97500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.97500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 130.38000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.97500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.97500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.46000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.97500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.97500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 130.38000 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 86.92000 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL UNIT CONTAINS PROTEIN REMARK 300 CHAIN A, AND DNA STRANDS B AND C. THE TRIMER (ACCORDING TO PDB REMARK 300 CONVENTIONS) IS A COMPLEX OF THE MONOMERIC METHYLTRANSFERASE WITH REMARK 300 ITS SUBSTRATE, DOUBLE STRANDED DNA. 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: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 785 LIES ON A SPECIAL POSITION. 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 GLU A 394 REMARK 465 GLU A 395 REMARK 465 LEU A 396 REMARK 465 GLU A 397 REMARK 465 HIS A 398 REMARK 465 HIS A 399 REMARK 465 HIS A 400 REMARK 465 HIS A 401 REMARK 465 HIS A 402 REMARK 465 HIS A 403 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. = -6.2 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 LYS A 60 -74.93 -90.96 REMARK 500 ASN A 61 61.93 -116.42 REMARK 500 SER A 80 -9.66 85.45 REMARK 500 SER A 80 -7.65 85.45 REMARK 500 PHE A 112 -66.17 69.26 REMARK 500 ASN A 290 13.18 81.89 REMARK 500 REMARK 500 REMARK: NULL 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PT6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MOUSE DNMT1(650-1602) IN COMPLEX WITH DNA REMARK 900 RELATED ID: 3PT9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MOUSE DNMT1(731-1602) IN THE FREE STATE REMARK 900 RELATED ID: 3PTA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN DNMT1(646-1600) IN COMPLEX WITH DNA REMARK 900 RELATED ID: 1MHT RELATED DB: PDB REMARK 900 COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S- REMARK 900 ADENOSYL-L-HOMOCYSTEINE REMARK 900 RELATED ID: 2C7P RELATED DB: PDB REMARK 900 HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING REMARK 900 2-AMINOPURINE OPPOSITE TO THE TARGET BASE (GCGC:GMPC) AND SAH REMARK 900 RELATED ID: 4DA4 RELATED DB: PDB REMARK 900 STRUCTURE OF MOUSE DNMT1 (731-1602) BOUND TO HEMIMETHYLATED CPG DNA REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THESE ARE NATURAL STRAIN VARIATIONS. DBREF 4DKJ A 1 395 UNP Q8EVR5 Q8EVR5_MYCPE 1 395 DBREF 4DKJ B 1 14 PDB 4DKJ 4DKJ 1 14 DBREF 4DKJ C 1 14 PDB 4DKJ 4DKJ 1 14 SEQADV 4DKJ ARG A 68 UNP Q8EVR5 GLN 68 SEE REMARK 999 SEQADV 4DKJ ARG A 71 UNP Q8EVR5 LYS 71 SEE REMARK 999 SEQADV 4DKJ PRO A 295 UNP Q8EVR5 SER 295 ENGINEERED MUTATION SEQADV 4DKJ LEU A 396 UNP Q8EVR5 EXPRESSION TAG SEQADV 4DKJ GLU A 397 UNP Q8EVR5 EXPRESSION TAG SEQADV 4DKJ HIS A 398 UNP Q8EVR5 EXPRESSION TAG SEQADV 4DKJ HIS A 399 UNP Q8EVR5 EXPRESSION TAG SEQADV 4DKJ HIS A 400 UNP Q8EVR5 EXPRESSION TAG SEQADV 4DKJ HIS A 401 UNP Q8EVR5 EXPRESSION TAG SEQADV 4DKJ HIS A 402 UNP Q8EVR5 EXPRESSION TAG SEQADV 4DKJ HIS A 403 UNP Q8EVR5 EXPRESSION TAG SEQRES 1 A 403 MET ASN SER ASN LYS ASP LYS ILE LYS VAL ILE LYS VAL SEQRES 2 A 403 PHE GLU ALA PHE ALA GLY ILE GLY SER GLN PHE LYS ALA SEQRES 3 A 403 LEU LYS ASN ILE ALA ARG SER LYS ASN TRP GLU ILE GLN SEQRES 4 A 403 HIS SER GLY MET VAL GLU TRP PHE VAL ASP ALA ILE VAL SEQRES 5 A 403 SER TYR VAL ALA ILE HIS SER LYS ASN PHE ASN PRO LYS SEQRES 6 A 403 ILE GLU ARG LEU ASP ARG ASP ILE LEU SER ILE SER ASN SEQRES 7 A 403 ASP SER LYS MET PRO ILE SER GLU TYR GLY ILE LYS LYS SEQRES 8 A 403 ILE ASN ASN THR ILE LYS ALA SER TYR LEU ASN TYR ALA SEQRES 9 A 403 LYS LYS HIS PHE ASN ASN LEU PHE ASP ILE LYS LYS VAL SEQRES 10 A 403 ASN LYS ASP ASN PHE PRO LYS ASN ILE ASP ILE PHE THR SEQRES 11 A 403 TYR SER PHE PRO CYS GLN ASP LEU SER VAL GLN GLY LEU SEQRES 12 A 403 GLN LYS GLY ILE ASP LYS GLU LEU ASN THR ARG SER GLY SEQRES 13 A 403 LEU LEU TRP GLU ILE GLU ARG ILE LEU GLU GLU ILE LYS SEQRES 14 A 403 ASN SER PHE SER LYS GLU GLU MET PRO LYS TYR LEU LEU SEQRES 15 A 403 MET GLU ASN VAL LYS ASN LEU LEU SER HIS LYS ASN LYS SEQRES 16 A 403 LYS ASN TYR ASN THR TRP LEU LYS GLN LEU GLU LYS PHE SEQRES 17 A 403 GLY TYR LYS SER LYS THR TYR LEU LEU ASN SER LYS ASN SEQRES 18 A 403 PHE ASP ASN CYS GLN ASN ARG GLU ARG VAL PHE CYS LEU SEQRES 19 A 403 SER ILE ARG ASP ASP TYR LEU GLU LYS THR GLY PHE LYS SEQRES 20 A 403 PHE LYS GLU LEU GLU LYS VAL LYS ASN PRO PRO LYS LYS SEQRES 21 A 403 ILE LYS ASP ILE LEU VAL ASP SER SER ASN TYR LYS TYR SEQRES 22 A 403 LEU ASN LEU ASN LYS TYR GLU THR THR THR PHE ARG GLU SEQRES 23 A 403 THR LYS SER ASN ILE ILE SER ARG PRO LEU LYS ASN TYR SEQRES 24 A 403 THR THR PHE ASN SER GLU ASN TYR VAL TYR ASN ILE ASN SEQRES 25 A 403 GLY ILE GLY PRO THR LEU THR ALA SER GLY ALA ASN SER SEQRES 26 A 403 ARG ILE LYS ILE GLU THR GLN GLN GLY VAL ARG TYR LEU SEQRES 27 A 403 THR PRO LEU GLU CYS PHE LYS TYR MET GLN PHE ASP VAL SEQRES 28 A 403 ASN ASP PHE LYS LYS VAL GLN SER THR ASN LEU ILE SER SEQRES 29 A 403 GLU ASN LYS MET ILE TYR ILE ALA GLY ASN SER ILE PRO SEQRES 30 A 403 VAL LYS ILE LEU GLU ALA ILE PHE ASN THR LEU GLU PHE SEQRES 31 A 403 VAL ASN ASN GLU GLU LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 14 DC DC DA DC DA DT DG C37 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 MODRES 4DKJ C37 B 8 DC MODRES 4DKJ 5CM C 7 DC HET C37 B 8 20 HET 5CM C 7 20 HET SAH A 501 26 HET GOL A 502 6 HETNAM C37 5-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 C37 C9 H13 F N3 O7 P FORMUL 3 5CM C10 H16 N3 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *267(H2 O) HELIX 1 1 GLY A 21 ALA A 31 1 11 HELIX 2 2 ARG A 32 LYS A 34 5 3 HELIX 3 3 PHE A 47 SER A 59 1 13 HELIX 4 4 SER A 85 ASN A 93 1 9 HELIX 5 5 THR A 95 PHE A 108 1 14 HELIX 6 6 ASP A 113 VAL A 117 5 5 HELIX 7 7 ASP A 148 ASN A 152 5 5 HELIX 8 8 ARG A 154 GLY A 156 5 3 HELIX 9 9 LEU A 157 PHE A 172 1 16 HELIX 10 10 SER A 173 MET A 177 5 5 HELIX 11 11 ASN A 188 LEU A 190 5 3 HELIX 12 12 SER A 191 PHE A 208 1 18 HELIX 13 13 LYS A 220 PHE A 222 5 3 HELIX 14 14 ASP A 238 GLY A 245 1 8 HELIX 15 15 GLU A 250 VAL A 254 5 5 HELIX 16 16 LYS A 260 LEU A 265 5 6 HELIX 17 17 PHE A 302 GLU A 305 5 4 HELIX 18 18 GLY A 322 ARG A 326 5 5 HELIX 19 19 THR A 339 MET A 347 1 9 HELIX 20 20 ASP A 350 THR A 360 1 11 HELIX 21 21 SER A 364 ASN A 374 1 11 HELIX 22 22 PRO A 377 THR A 387 1 11 SHEET 1 A 6 TRP A 36 VAL A 44 0 SHEET 2 A 6 LYS A 9 ALA A 16 1 N ILE A 11 O GLU A 37 SHEET 3 A 6 ILE A 128 TYR A 131 1 O ILE A 128 N PHE A 14 SHEET 4 A 6 TYR A 180 VAL A 186 1 O TYR A 180 N PHE A 129 SHEET 5 A 6 GLU A 229 ARG A 237 -1 O SER A 235 N LEU A 181 SHEET 6 A 6 TYR A 210 ASN A 218 -1 N LYS A 211 O ILE A 236 SHEET 1 B 5 ARG A 285 GLU A 286 0 SHEET 2 B 5 ILE A 292 PRO A 295 -1 O SER A 293 N ARG A 285 SHEET 3 B 5 TYR A 307 ASN A 310 -1 O ASN A 310 N ILE A 292 SHEET 4 B 5 LYS A 328 THR A 331 1 O LYS A 328 N TYR A 309 SHEET 5 B 5 GLY A 334 TYR A 337 -1 O ARG A 336 N ILE A 329 LINK O3' DG B 7 P C37 B 8 1555 1555 1.61 LINK O3' C37 B 8 P DG B 9 1555 1555 1.61 LINK O3' DG C 6 P 5CM C 7 1555 1555 1.61 LINK O3' 5CM C 7 P DG C 8 1555 1555 1.62 SITE 1 AC1 23 PHE A 17 ALA A 18 GLY A 19 ILE A 20 SITE 2 AC1 23 GLY A 21 SER A 22 GLN A 23 GLU A 45 SITE 3 AC1 23 TRP A 46 PHE A 47 SER A 80 PHE A 112 SITE 4 AC1 23 ASP A 113 ILE A 114 SER A 132 ARG A 154 SITE 5 AC1 23 LEU A 157 ASN A 374 SER A 375 HOH A 612 SITE 6 AC1 23 HOH A 625 HOH A 655 C37 B 8 SITE 1 AC2 9 TYR A 337 ASN A 366 ILE A 369 HOH A 613 SITE 2 AC2 9 HOH A 616 HOH A 633 HOH A 650 HOH A 651 SITE 3 AC2 9 DA C 5 CRYST1 83.950 83.950 173.840 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 0.011912 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011912 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005752 0.00000