HEADER TRANSFERASE/DNA 27-NOV-05 2C7Q TITLE HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2- TITLE 2 AMINOPURINE OUTSIDE THE RECOGNITION SEQUENCE (PAIRED WITH G) 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(*T*GP*GP*(2PR)*GP*GP*(5CM)*GP*CP*TP*GP* AP*C)-3'; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*T*GP*TP*CP*AP*GP*CP*GP*CP*CP*GP*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 D.DAUJOTYTE,S.GRAZULIS REVDAT 6 13-DEC-23 2C7Q 1 REMARK REVDAT 5 24-JUL-19 2C7Q 1 REMARK LINK REVDAT 4 29-JAN-14 2C7Q 1 HEADER TITLE COMPND SOURCE REVDAT 4 2 1 KEYWDS REMARK VERSN SEQRES REVDAT 4 3 1 MODRES HET HETNAM HETSYN REVDAT 4 4 1 FORMUL LINK HETATM REVDAT 3 24-FEB-09 2C7Q 1 VERSN REVDAT 2 18-JAN-06 2C7Q 1 JRNL REVDAT 1 14-DEC-05 2C7Q 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 50617366.940 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 45794 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) : 0.187 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4631 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6523 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 720 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 : 2574 REMARK 3 NUCLEIC ACID ATOMS : 512 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 366 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.14000 REMARK 3 B22 (A**2) : 1.14000 REMARK 3 B33 (A**2) : -2.28000 REMARK 3 B12 (A**2) : 0.77000 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) : 0.21 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) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 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) : 0.470 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.790 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.670 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 56.70 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 2C7Q 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_1290026566. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-04 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 : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.050 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 45796 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 31.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 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 (%): 54.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CITRATE PH 5.6, 1.6 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 47.55000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.45301 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 104.06000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.55000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.45301 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 104.06000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.55000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.45301 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 104.06000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.55000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.45301 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 104.06000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.55000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.45301 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 104.06000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.55000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.45301 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 104.06000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 54.90601 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 208.12000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 54.90601 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 208.12000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 54.90601 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 208.12000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 54.90601 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 208.12000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 54.90601 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 208.12000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 54.90601 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 208.12000 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.8 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 A2139 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 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 DT D 421 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 3 CG CD OE1 OE2 REMARK 470 LYS A 5 CE NZ REMARK 470 GLU A 55 OE1 OE2 REMARK 470 LYS A 67 NZ REMARK 470 LYS A 91 NZ REMARK 470 ARG A 109 NE CZ NH1 NH2 REMARK 470 GLN A 178 CD OE1 NE2 REMARK 470 LYS A 184 CD CE NZ REMARK 470 ILE A 207 CG1 CD1 REMARK 470 LYS A 210 CD CE NZ REMARK 470 GLN A 217 CD OE1 NE2 REMARK 470 GLN A 221 CG CD OE1 NE2 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 2037 O HOH A 2272 1.92 REMARK 500 O HOH A 2273 O HOH A 2274 1.99 REMARK 500 O HOH A 2262 O HOH A 2264 2.05 REMARK 500 O HOH A 2051 O HOH A 2277 2.06 REMARK 500 O HOH A 2030 O HOH A 2262 2.14 REMARK 500 O HOH A 2078 O HOH A 2104 2.14 REMARK 500 O HOH A 2030 O HOH A 2260 2.16 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 2008 O HOH A 2266 10455 1.66 REMARK 500 O HOH A 2009 O HOH A 2266 10455 1.78 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. = -15.2 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 TYR A 37 142.27 -170.23 REMARK 500 ASP A 60 101.62 -8.16 REMARK 500 LYS A 112 63.06 38.41 REMARK 500 ASP A 144 42.33 77.11 REMARK 500 LYS A 162 48.46 -82.66 REMARK 500 PRO A 224 47.72 -77.90 REMARK 500 PHE A 259 48.14 -107.58 REMARK 500 LYS A 261 -8.57 71.01 REMARK 500 SER A 305 -167.95 -72.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2288 DISTANCE = 5.87 ANGSTROMS 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 SAH A 1328 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 1332 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: 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 2C7Q A 1 327 UNP P05102 MTH1_HAEHA 1 327 DBREF 2C7Q C 401 413 PDB 2C7Q 2C7Q 401 413 DBREF 2C7Q D 421 433 PDB 2C7Q 2C7Q 421 433 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 13 DT DG DG 2PR DG DG 5CM DG DC DT DG DA DC SEQRES 1 D 13 DT DG DT DC DA DG DC DG DC DC DG DC DC MODRES 2C7Q 2PR C 404 DG MODRES 2C7Q 5CM C 407 DC HET 2PR C 404 21 HET 5CM C 407 20 HET SAH A1328 26 HET SO4 A1329 5 HET SO4 A1330 5 HET SO4 A1331 5 HET CIT A1332 13 HETNAM 2PR 2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'- HETNAM 2 2PR MONOPHOSPHATE HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM SO4 SULFATE ION HETNAM CIT CITRIC ACID HETSYN 2PR 2-AMINOPURINE-2'-DEOXYRIBO-5'-MONOPHOSPHATE FORMUL 2 2PR C10 H14 N5 O6 P FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 SO4 3(O4 S 2-) FORMUL 8 CIT C6 H8 O7 FORMUL 9 HOH *366(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 196 1 6 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 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 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 403 P 2PR C 404 1555 1555 1.60 LINK O3' 2PR C 404 P DG C 405 1555 1555 1.61 LINK O3' DG C 406 P 5CM C 407 1555 1555 1.60 LINK O3' 5CM C 407 P DG C 408 1555 1555 1.60 SITE 1 AC1 6 PRO A 198 ASP A 199 HOH A2230 HOH A2299 SITE 2 AC1 6 HOH A2300 HOH A2301 SITE 1 AC2 5 PRO A 286 ASP A 287 SER A 288 HOH A2233 SITE 2 AC2 5 HOH A2302 SITE 1 AC3 5 LYS A 193 ARG A 245 LYS A 290 HOH A2203 SITE 2 AC3 5 HOH A2303 SITE 1 AC4 23 PHE A 18 ALA A 19 GLY A 20 LEU A 21 SITE 2 AC4 23 GLY A 23 ASN A 39 GLU A 40 TRP A 41 SITE 3 AC4 23 ASP A 42 ASP A 60 ILE A 61 GLY A 78 SITE 4 AC4 23 PRO A 80 ASN A 304 SER A 305 VAL A 306 SITE 5 AC4 23 HOH A2068 HOH A2246 HOH A2248 HOH A2294 SITE 6 AC4 23 HOH A2295 HOH A2296 HOH A2297 SITE 1 AC5 8 LYS A 150 VAL A 151 LEU A 152 ASN A 153 SITE 2 AC5 8 ASP A 156 PRO A 185 HOH A2121 HOH A2145 CRYST1 95.100 95.100 312.180 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 0.010515 0.006071 0.000000 0.00000 SCALE2 0.000000 0.012142 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003203 0.00000