HEADER TRANSFERASE/DNA 27-NOV-05 2C7R TITLE HHAI DNA METHYLTRANSFERASE (T250G MUTANT) COMPLEX WITH OLIGONUCLEOTIDE TITLE 2 CONTAINING 2-AMINOPURINE AS A TARGET BASE (GPGC:GMGC) AND SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: MODIFICATION METHYLASE HHAI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA METHYLTRANSFERASE HHAI, CYTOSINE-SPECIFIC COMPND 5 METHYLTRANSFERASE HHAI; COMPND 6 EC: 2.1.1.37; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*G*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP*C)-3'; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*G*TP*CP*AP*GP*(2PR)*GP*CP*AP*TP*CP*C)-3'; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS HAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 726; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ER1727; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PHH552; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS BASE FLIPPING, RESTRICTION SYSTEM, TRANSFERASE-DNA COMPLEX, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.DAUJOTYTE,S.GRAZULIS REVDAT 4 13-DEC-23 2C7R 1 REMARK LINK REVDAT 3 29-JAN-14 2C7R 1 HEADER COMPND SOURCE KEYWDS REVDAT 3 2 1 REMARK VERSN SEQRES MODRES REVDAT 3 3 1 HET HETNAM HETSYN FORMUL REVDAT 3 4 1 LINK HETATM REVDAT 2 24-FEB-09 2C7R 1 VERSN REVDAT 1 14-DEC-05 2C7R 0 JRNL AUTH R.K.NEELY,D.DAUJOTYTE,S.GRAZULIS,S.W.MAGENNIS,D.T.F.DRYDEN, JRNL AUTH 2 S.KLIMASAUSKAS,A.C.JONES JRNL TITL TIME-RESOLVED FLUORESCENCE OF 2-AMINOPURINE AS A PROBE OF JRNL TITL 2 BASE FLIPPING IN M.HHAI-DNA COMPLEXES. JRNL REF NUCLEIC ACIDS RES. V. 33 6953 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 16340006 JRNL DOI 10.1093/NAR/GKI995 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 32993147.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 44234 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 SET) : 0.199 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4476 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6512 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 750 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2603 REMARK 3 NUCLEIC ACID ATOMS : 497 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 271 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.13000 REMARK 3 B22 (A**2) : 1.13000 REMARK 3 B33 (A**2) : -2.26000 REMARK 3 B12 (A**2) : 0.87000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.160 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.820 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.310 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.280 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.010 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 46.61 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : 2AP.PAR REMARK 3 PARAMETER FILE 5 : 5MC.PAR REMARK 3 PARAMETER FILE 6 : GOL.PAR REMARK 3 PARAMETER FILE 7 : SAH.PAR REMARK 3 PARAMETER FILE 8 : SO4.PAR REMARK 3 PARAMETER FILE 9 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : 2AP.TOP REMARK 3 TOPOLOGY FILE 5 : 5MC.TOP REMARK 3 TOPOLOGY FILE 6 : GOL.TOP REMARK 3 TOPOLOGY FILE 7 : SAH.TOP REMARK 3 TOPOLOGY FILE 8 : SO4.TOP REMARK 3 TOPOLOGY FILE 9 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESOLUTION-DEPENDENT WEIGHTING SCHEME REMARK 3 USED. BULK SOLVENT MODEL USED. REMARK 4 REMARK 4 2C7R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1290026567. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9755 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44234 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3MHT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CITRATE PH 5.6, 1.7 M REMARK 280 AMMONIUM SULFATE, 5 % GLUCOSE, PH 5.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 47.81000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.60312 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 105.25200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.81000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.60312 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 105.25200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.81000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.60312 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 105.25200 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.81000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.60312 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 105.25200 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.81000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.60312 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 105.25200 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.81000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.60312 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 105.25200 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 55.20623 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 210.50400 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 55.20623 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 210.50400 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 55.20623 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 210.50400 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 55.20623 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 210.50400 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 55.20623 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 210.50400 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 55.20623 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 210.50400 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: THE OLIGOMERIC STATE OF HHAI METHYLTRANSFERASE REMARK 300 IS MONOMERIC, BUT SINCE IN THIS ENTRY, THE REMARK 300 PROTEIN IS IN COMPLEX WITH DNA, THE QUATERNARY REMARK 300 STRUCTURE FOR THIS ENTRY IS MARKED AS TRIMERIC. 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 A2105 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 RECOGNIZES THE DOUBLE-STRANDED SEQUENCE GCGC, CAUSES REMARK 400 SPECIFIC METHYLATION AND PROTECTS THE DNA FROM REMARK 400 CLEAVAGE BY THE HHAI ENDONUCLEASE. REMARK 400 REMARK 400 ENGINEERED RESIDUE IN CHAIN A, THR 250 TO GLY 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 O HOH A 2066 O HOH A 2067 1.67 REMARK 500 O HOH A 2025 O HOH A 2186 2.06 REMARK 500 NE2 GLN A 221 O HOH A 2134 2.09 REMARK 500 O HOH A 2007 O HOH A 2194 2.11 REMARK 500 CE LYS A 111 O HOH A 2066 2.17 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 A 220 C GLN A 221 N -0.244 REMARK 500 GLN A 221 C THR A 222 N -0.172 REMARK 500 DG C 402 P DG C 402 OP3 -0.078 REMARK 500 DG D 422 P DG D 422 OP3 -0.083 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 GLU A 220 CA - C - N ANGL. DEV. = 16.9 DEGREES REMARK 500 GLU A 220 O - C - N ANGL. DEV. = -18.1 DEGREES REMARK 500 GLN A 221 C - N - CA ANGL. DEV. = 27.0 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 TYR A 37 142.21 -170.59 REMARK 500 ASP A 60 105.49 -7.87 REMARK 500 ASP A 144 46.86 78.07 REMARK 500 LYS A 261 -37.33 69.67 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 DC C 409 0.07 SIDE CHAIN REMARK 500 DC D 432 0.07 SIDE CHAIN 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 SO4 A 1329 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1330 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1331 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1333 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1335 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 1328 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1336 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1338 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1339 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1340 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 10MH RELATED DB: PDB REMARK 900 TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND REMARK 900 HEMIMETHYLATED DEOXYRIBONUCLEIC ACID CONTAINING 5,6-DIHYDRO-5- REMARK 900 AZACYTOSINE AT THE TARGET REMARK 900 RELATED ID: 1FJX RELATED DB: PDB REMARK 900 STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASEMUTANT (T250G) REMARK 900 IN COMPLEX WITH DNA AND ADOHCY REMARK 900 RELATED ID: 1HMY RELATED DB: PDB REMARK 900 HHAI DEOXYRIBONUCLEIC ACID (CYTOSINE-C5-)- METHYLTRANSFERASE REMARK 900 COMPLEX WITH S-ADENOSYL-L- METHIONINE REMARK 900 RELATED ID: 1M0E RELATED DB: PDB REMARK 900 ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS ACOVALENT REMARK 900 COMPLEX WITH DNA METHYLTRANSFERASE REMARK 900 RELATED ID: 1MHT RELATED DB: PDB REMARK 900 COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, REMARK 900 DEOXYRIBONUCLEIC ACID AND S- ADENOSYL-L-HOMOCYSTEINE REMARK 900 RELATED ID: 1SKM RELATED DB: PDB REMARK 900 HHAI METHYLTRANSFERASE IN COMPLEX WITH DNA CONTAINING ANABASIC REMARK 900 SOUTH CARBOCYCLIC SUGAR AT ITS TARGET SITE REMARK 900 RELATED ID: 1SVU RELATED DB: PDB REMARK 900 STRUCTURE OF THE Q237W MUTANT OF HHAI DNAMETHYLTRANSFERASE: AN REMARK 900 INSIGHT INTO PROTEIN- PROTEININTERACTIONS REMARK 900 RELATED ID: 2HMY RELATED DB: PDB REMARK 900 BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH ADOMET FORMED IN THE REMARK 900 PRESENCE OF A SHORT NONPSECIFIC DEOXYRIBONUCLEIC ACID REMARK 900 OLIGONUCLEOTIDE REMARK 900 RELATED ID: 3MHT RELATED DB: PDB REMARK 900 TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH UNMODIFIED REMARK 900 DEOXYRIBONUCLEIC ACID AND ADOHCY REMARK 900 RELATED ID: 4MHT RELATED DB: PDB REMARK 900 TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH NATIVE REMARK 900 DEOXYRIBONUCLEIC ACID AND ADOHCY REMARK 900 RELATED ID: 5MHT RELATED DB: PDB REMARK 900 TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH HEMIMETHYLATED REMARK 900 DEOXYRIBONUCLEIC ACID AND ADOHCY REMARK 900 RELATED ID: 6MHT RELATED DB: PDB REMARK 900 TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND REMARK 900 DEOXYRIBONUCLEIC ACID CONTAINING 4'-THIO-2'DEOXYCYTIDINE AT THE REMARK 900 TARGET REMARK 900 RELATED ID: 7MHT RELATED DB: PDB REMARK 900 CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID REMARK 900 COMPLEX REMARK 900 RELATED ID: 8MHT RELATED DB: PDB REMARK 900 CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID REMARK 900 COMPLEX REMARK 900 RELATED ID: 9MHT RELATED DB: PDB REMARK 900 CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/ DEOXYRIBONUCLEIC ACID REMARK 900 COMPLEX REMARK 900 RELATED ID: 2C7O RELATED DB: PDB REMARK 900 HHAI DNA METHYLTRANSFERASE COMPLEX WITH 13MER OLIGONUCLEOTIDE REMARK 900 CONTAINING 2-AMINOPURINE ADJACENT TO THE TARGET BASE (PCGC:GMGC) REMARK 900 AND SAH 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: 2C7Q RELATED DB: PDB REMARK 900 HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING REMARK 900 2-AMINOPURINE OUTSIDE THE RECOGNITION SEQUENCE (PAIRED WITH G) AND REMARK 900 SAH DBREF 2C7R A 1 327 UNP P05102 MTH1_HAEHA 1 327 DBREF 2C7R C 402 413 PDB 2C7R 2C7R 402 413 DBREF 2C7R D 422 433 PDB 2C7R 2C7R 422 433 SEQADV 2C7R GLY A 250 UNP P05102 THR 250 ENGINEERED MUTATION SEQRES 1 A 327 MET ILE GLU ILE LYS ASP LYS GLN LEU THR GLY LEU ARG SEQRES 2 A 327 PHE ILE ASP LEU PHE ALA GLY LEU GLY GLY PHE ARG LEU SEQRES 3 A 327 ALA LEU GLU SER CYS GLY ALA GLU CYS VAL TYR SER ASN SEQRES 4 A 327 GLU TRP ASP LYS TYR ALA GLN GLU VAL TYR GLU MET ASN SEQRES 5 A 327 PHE GLY GLU LYS PRO GLU GLY ASP ILE THR GLN VAL ASN SEQRES 6 A 327 GLU LYS THR ILE PRO ASP HIS ASP ILE LEU CYS ALA GLY SEQRES 7 A 327 PHE PRO CYS GLN ALA PHE SER ILE SER GLY LYS GLN LYS SEQRES 8 A 327 GLY PHE GLU ASP SER ARG GLY THR LEU PHE PHE ASP ILE SEQRES 9 A 327 ALA ARG ILE VAL ARG GLU LYS LYS PRO LYS VAL VAL PHE SEQRES 10 A 327 MET GLU ASN VAL LYS ASN PHE ALA SER HIS ASP ASN GLY SEQRES 11 A 327 ASN THR LEU GLU VAL VAL LYS ASN THR MET ASN GLU LEU SEQRES 12 A 327 ASP TYR SER PHE HIS ALA LYS VAL LEU ASN ALA LEU ASP SEQRES 13 A 327 TYR GLY ILE PRO GLN LYS ARG GLU ARG ILE TYR MET ILE SEQRES 14 A 327 CYS PHE ARG ASN ASP LEU ASN ILE GLN ASN PHE GLN PHE SEQRES 15 A 327 PRO LYS PRO PHE GLU LEU ASN THR PHE VAL LYS ASP LEU SEQRES 16 A 327 LEU LEU PRO ASP SER GLU VAL GLU HIS LEU VAL ILE ASP SEQRES 17 A 327 ARG LYS ASP LEU VAL MET THR ASN GLN GLU ILE GLU GLN SEQRES 18 A 327 THR THR PRO LYS THR VAL ARG LEU GLY ILE VAL GLY LYS SEQRES 19 A 327 GLY GLY GLN GLY GLU ARG ILE TYR SER THR ARG GLY ILE SEQRES 20 A 327 ALA ILE GLY LEU SER ALA TYR GLY GLY GLY ILE PHE ALA SEQRES 21 A 327 LYS THR GLY GLY TYR LEU VAL ASN GLY LYS THR ARG LYS SEQRES 22 A 327 LEU HIS PRO ARG GLU CYS ALA ARG VAL MET GLY TYR PRO SEQRES 23 A 327 ASP SER TYR LYS VAL HIS PRO SER THR SER GLN ALA TYR SEQRES 24 A 327 LYS GLN PHE GLY ASN SER VAL VAL ILE ASN VAL LEU GLN SEQRES 25 A 327 TYR ILE ALA TYR ASN ILE GLY SER SER LEU ASN PHE LYS SEQRES 26 A 327 PRO TYR SEQRES 1 C 12 DG DG DA DT DG 5CM DG DC DT DG DA DC SEQRES 1 D 12 DG DT DC DA DG 2PR DG DC DA DT DC DC MODRES 2C7R 5CM C 407 DC MODRES 2C7R 2PR D 427 DG HET 5CM C 407 20 HET 2PR D 427 21 HET SAH A1328 26 HET SO4 A1329 5 HET SO4 A1330 5 HET SO4 A1331 5 HET SO4 A1332 5 HET SO4 A1333 5 HET SO4 A1334 5 HET SO4 A1335 5 HET GOL A1336 6 HET GOL A1337 6 HET GOL A1338 6 HET GOL A1339 6 HET GOL A1340 6 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM 2PR 2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'- HETNAM 2 2PR MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN 2PR 2-AMINOPURINE-2'-DEOXYRIBO-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 3 2PR C10 H14 N5 O6 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 SO4 7(O4 S 2-) FORMUL 12 GOL 5(C3 H8 O3) FORMUL 17 HOH *271(H2 O) HELIX 1 1 GLY A 22 CYS A 31 1 10 HELIX 2 2 ASP A 42 GLY A 54 1 13 HELIX 3 3 ASP A 60 VAL A 64 5 5 HELIX 4 4 ASN A 65 ILE A 69 5 5 HELIX 5 5 LYS A 91 ASP A 95 5 5 HELIX 6 6 LEU A 100 LYS A 112 1 13 HELIX 7 7 ASN A 123 SER A 126 5 4 HELIX 8 8 GLY A 130 LEU A 143 1 14 HELIX 9 9 LEU A 155 GLY A 158 5 4 HELIX 10 10 ASN A 173 ASN A 176 5 4 HELIX 11 11 PHE A 191 LEU A 195 5 5 HELIX 12 12 PRO A 198 VAL A 202 5 5 HELIX 13 13 VAL A 202 LEU A 205 5 4 HELIX 14 14 HIS A 275 MET A 283 1 9 HELIX 15 15 SER A 294 SER A 305 1 12 HELIX 16 16 VAL A 307 PHE A 324 1 18 SHEET 1 AA 6 GLU A 34 SER A 38 0 SHEET 2 AA 6 ARG A 13 LEU A 17 1 O PHE A 14 N VAL A 36 SHEET 3 AA 6 ILE A 74 GLY A 78 1 O ILE A 74 N ILE A 15 SHEET 4 AA 6 VAL A 115 VAL A 121 1 O VAL A 115 N LEU A 75 SHEET 5 AA 6 GLU A 164 PHE A 171 -1 O ILE A 166 N ASN A 120 SHEET 6 AA 6 HIS A 148 ASN A 153 -1 O HIS A 148 N ILE A 169 SHEET 1 AB 5 VAL A 213 MET A 214 0 SHEET 2 AB 5 ARG A 228 ILE A 231 -1 O ILE A 231 N VAL A 213 SHEET 3 AB 5 ARG A 240 SER A 243 -1 O ILE A 241 N LEU A 229 SHEET 4 AB 5 GLY A 264 VAL A 267 1 O GLY A 264 N TYR A 242 SHEET 5 AB 5 LYS A 270 LYS A 273 -1 O LYS A 270 N VAL A 267 LINK O3' DG C 406 P 5CM C 407 1555 1555 1.61 LINK O3' 5CM C 407 P DG C 408 1555 1555 1.60 LINK O3' DG D 426 P 2PR D 427 1555 1555 1.60 LINK O3' 2PR D 427 P DG D 428 1555 1555 1.60 SITE 1 AC1 6 ASP A 199 HOH A2118 HOH A2172 HOH A2218 SITE 2 AC1 6 HOH A2219 HOH A2220 SITE 1 AC2 3 PRO A 286 ASP A 287 SER A 288 SITE 1 AC3 5 LYS A 193 ARG A 245 LYS A 290 HOH A2151 SITE 2 AC3 5 HOH A2173 SITE 1 AC4 4 LEU A 196 LEU A 197 PRO A 198 ARG A 281 SITE 1 AC5 3 LYS A 114 ARG A 172 HOH A2222 SITE 1 AC6 2 GLU A 220 GLN A 221 SITE 1 AC7 3 MET A 51 GLY A 269 PRO A 293 SITE 1 AC8 24 PHE A 18 ALA A 19 LEU A 21 GLY A 23 SITE 2 AC8 24 ASN A 39 GLU A 40 TRP A 41 ASP A 42 SITE 3 AC8 24 ASP A 60 ILE A 61 GLY A 78 PRO A 80 SITE 4 AC8 24 LEU A 100 TYR A 285 ASN A 304 SER A 305 SITE 5 AC8 24 VAL A 306 HOH A2043 HOH A2189 HOH A2191 SITE 6 AC8 24 HOH A2213 HOH A2215 HOH A2216 HOH A2217 SITE 1 AC9 9 LYS A 150 VAL A 151 LEU A 152 ASN A 153 SITE 2 AC9 9 ASP A 156 TYR A 157 PRO A 185 HOH A2084 SITE 3 AC9 9 HOH A2224 SITE 1 BC1 6 GLU A 3 ILE A 4 LYS A 5 ASP A 6 SITE 2 BC1 6 TYR A 316 TYR A 327 SITE 1 BC2 4 TYR A 316 LYS A 325 PRO A 326 TYR A 327 SITE 1 BC3 10 GLN A 237 GLY A 238 GLY A 250 LYS A 261 SITE 2 BC3 10 THR A 262 GLY A 263 HOH A2148 HOH A2149 SITE 3 BC3 10 HOH A2153 HOH A2225 SITE 1 BC4 7 GLU A 203 HIS A 275 HOH A2218 HOH A2226 SITE 2 BC4 7 HOH A2227 HOH A2228 HOH A2229 CRYST1 95.620 95.620 315.756 90.00 90.00 120.00 H 3 2 18 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 0.010458 0.006038 0.000000 0.00000 SCALE2 0.000000 0.012076 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003167 0.00000