PDB Short entry for 2C7P HEADER TRANSFERASE/DNA 25-NOV-05 2C7P TITLE HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2- TITLE 2 AMINOPURINE OPPOSITE TO THE TARGET BASE (GCGC:GMPC) 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 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*G*GP*AP*TP*GP*(5CM*2PR)*CP*TP*GP*AP*C)-3'; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*G*TP*CP*AP*GP*CP*GP*CP*AP*TP*CP*C)-3'; COMPND 14 CHAIN: D; COMPND 15 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: PHH553; 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 EXPDTA X-RAY DIFFRACTION AUTHOR R.K.NEELY,D.DAUJOTYTE,S.GRAZULIS,S.W.MAGENNIS,D.T.F.DRYDEN, AUTHOR 2 S.KLIMASAUSKAS,A.C.JONES REVDAT 5 13-DEC-23 2C7P 1 REMARK REVDAT 4 24-JUL-19 2C7P 1 REMARK LINK REVDAT 3 29-JAN-14 2C7P 1 HEADER TITLE COMPND SOURCE REVDAT 3 2 1 KEYWDS REMARK VERSN SEQRES REVDAT 3 3 1 MODRES HET HETNAM HETSYN REVDAT 3 4 1 FORMUL LINK HETATM REVDAT 2 24-FEB-09 2C7P 1 VERSN REVDAT 1 14-DEC-05 2C7P 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 30839027.080 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 59771 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) : 0.196 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6014 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8778 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 938 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.008 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2606 REMARK 3 NUCLEIC ACID ATOMS : 494 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 291 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.19000 REMARK 3 B22 (A**2) : 1.19000 REMARK 3 B33 (A**2) : -2.38000 REMARK 3 B12 (A**2) : 0.98000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.080 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) : 0.550 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.940 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.760 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.280 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 57.47 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 : CIT.PAR REMARK 3 PARAMETER FILE 7 : SAH.PAR REMARK 3 PARAMETER FILE 8 : SO4.PAR REMARK 3 PARAMETER FILE 9 : EPE.PAR REMARK 3 PARAMETER FILE 10 : 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 : CIT.TOP REMARK 3 TOPOLOGY FILE 7 : SAH.TOP REMARK 3 TOPOLOGY FILE 8 : SO4.TOP REMARK 3 TOPOLOGY FILE 9 : EPE.TOP REMARK 3 TOPOLOGY FILE 10 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESOLUTION-DEPENDENT WEIGHTING SCHEME REMARK 3 USED. BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2C7P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1290026565. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-02 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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8120 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS 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 : 59771 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 56.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.5000 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) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 (%): 55.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CITRATE PH 5.6, 1.4 M REMARK 280 AMMONIUM SULFATE, 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 47.42250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.37939 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 104.34333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.42250 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.37939 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 104.34333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.42250 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.37939 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 104.34333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.42250 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.37939 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 104.34333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.42250 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.37939 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 104.34333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.42250 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.37939 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 104.34333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 54.75879 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 208.68667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 54.75879 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 208.68667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 54.75879 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 208.68667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 54.75879 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 208.68667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 54.75879 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 208.68667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 54.75879 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 208.68667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.2 KCAL/MOL 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 A2107 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 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 2236 O HOH A 2237 0.12 REMARK 500 O HOH D 2017 O HOH D 2018 0.15 REMARK 500 O HOH A 2140 O HOH A 2141 0.17 REMARK 500 O HOH A 2126 O HOH A 2127 0.17 REMARK 500 O HOH A 2065 O HOH A 2066 0.24 REMARK 500 O HOH C 2027 O HOH C 2028 0.24 REMARK 500 O HOH A 2182 O HOH C 2015 1.52 REMARK 500 O HOH A 2155 O HOH A 2165 1.76 REMARK 500 O HOH A 2077 O HOH C 2002 2.12 REMARK 500 O HOH A 2134 O HOH A 2226 2.13 REMARK 500 O HOH C 2032 O HOH C 2034 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2037 O HOH A 2143 3455 0.28 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 DG C 402 P DG C 402 OP3 -0.080 REMARK 500 DG D 422 P DG D 422 OP3 -0.082 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 GLY A 78 N - CA - C ANGL. DEV. = -15.5 DEGREES REMARK 500 DC C 409 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC C 409 O4' - C1' - N1 ANGL. DEV. = 1.8 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 ASP A 60 101.87 -9.47 REMARK 500 ALA A 77 110.77 -162.63 REMARK 500 LYS A 112 64.44 35.90 REMARK 500 ASP A 144 42.97 75.55 REMARK 500 PHE A 259 46.39 -104.85 REMARK 500 LYS A 261 -8.72 64.77 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 DG D 422 0.05 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 SAH A 1328 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 1335 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: 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 REMARK 900 RELATED ID: 2C7R RELATED DB: PDB REMARK 900 HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING REMARK 900 2-AMINOPURINE AS A TARGET BASE (GPGC:GMGC) AND SAH DBREF 2C7P A 1 327 UNP P05102 MTH1_HAEHA 1 327 DBREF 2C7P C 402 413 PDB 2C7P 2C7P 402 413 DBREF 2C7P D 422 433 PDB 2C7P 2C7P 422 433 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 THR 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 2PR DC DT DG DA DC SEQRES 1 D 12 DG DT DC DA DG DC DG DC DA DT DC DC MODRES 2C7P 5CM C 407 DC MODRES 2C7P 2PR C 408 DG HET 5CM C 407 20 HET 2PR C 408 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 EPE A1334 15 HET CIT A1335 13 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 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM CIT CITRIC ACID HETSYN 2PR 2-AMINOPURINE-2'-DEOXYRIBO-5'-MONOPHOSPHATE HETSYN EPE HEPES FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 2 2PR C10 H14 N5 O6 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 SO4 5(O4 S 2-) FORMUL 10 EPE C8 H18 N2 O4 S FORMUL 11 CIT C6 H8 O7 FORMUL 12 HOH *291(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 THR A 99 LYS A 112 1 14 HELIX 7 7 ASN A 123 ASN A 129 5 7 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 HIS A 204 5 3 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 ASN A 39 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 6 VAL A 206 ILE A 207 0 SHEET 2 AB 6 LYS A 270 LYS A 273 -1 O THR A 271 N ILE A 207 SHEET 3 AB 6 GLY A 264 VAL A 267 -1 O TYR A 265 N ARG A 272 SHEET 4 AB 6 ARG A 240 SER A 243 1 O ARG A 240 N GLY A 264 SHEET 5 AB 6 ARG A 228 ILE A 231 -1 N LEU A 229 O ILE A 241 SHEET 6 AB 6 VAL A 213 MET A 214 -1 O VAL A 213 N ILE A 231 LINK O3' DG C 406 P 5CM C 407 1555 1555 1.60 LINK O3' 5CM C 407 P 2PR C 408 1555 1555 1.60 LINK O3' 2PR C 408 P DC C 409 1555 1555 1.61 SITE 1 AC1 4 PRO A 286 ASP A 287 SER A 288 HOH A2191 SITE 1 AC2 4 LEU A 196 LEU A 197 PRO A 198 ARG A 281 SITE 1 AC3 3 LYS A 193 ARG A 245 LYS A 290 SITE 1 AC4 3 LYS A 114 ARG A 172 HOH A2231 SITE 1 AC5 6 ASP A 199 HOH A2189 HOH A2233 HOH A2234 SITE 2 AC5 6 HOH A2236 HOH A2237 SITE 1 AC6 23 PHE A 18 ALA A 19 GLY A 20 LEU A 21 SITE 2 AC6 23 GLY A 23 ASN A 39 GLU A 40 TRP A 41 SITE 3 AC6 23 ASP A 60 ILE A 61 GLY A 78 PRO A 80 SITE 4 AC6 23 TYR A 285 ASN A 304 SER A 305 VAL A 306 SITE 5 AC6 23 HOH A2049 HOH A2202 HOH A2204 HOH A2227 SITE 6 AC6 23 HOH A2228 HOH A2229 HOH A2230 SITE 1 AC7 9 GLU A 3 ILE A 4 LYS A 5 ASP A 6 SITE 2 AC7 9 TYR A 316 LYS A 325 PRO A 326 TYR A 327 SITE 3 AC7 9 HOH A2216 SITE 1 AC8 10 LYS A 150 VAL A 151 LEU A 152 ASN A 153 SITE 2 AC8 10 ASP A 156 TYR A 157 PRO A 185 HOH A2100 SITE 3 AC8 10 HOH A2111 HOH A2238 CRYST1 94.845 94.845 313.030 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 0.010544 0.006087 0.000000 0.00000 SCALE2 0.000000 0.012175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003195 0.00000