PDB Short entry for 2UYC HEADER TRANSFERASE 03-APR-07 2UYC TITLE HHAI DNA METHYLTRANSFERASE R163N MUTANT COMPLEX WITH 13MER GCGC-GMGC TITLE 2 OLIGONUCLEOTIDE AND SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: MODIFICATION METHYLASE HHAI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI, MHHAI, HHAI DNA COMPND 5 METHYLTRANSFERASE; 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(*TP*GP*GP*AP*TP*GP*5CMP*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(*GP*TP*CP*AP*GP*CP*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: ER2267; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PHH5.3; 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 TRANSFERASE, S-ADENOSYL-L-METHIONINE, BASE FLIPPING, KEYWDS 2 METHYLTRANSFERASE, RESTRICTION SYSTEM, DNA METHYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.DAUJOTYTE,S.GRAZULIS REVDAT 5 13-DEC-23 2UYC 1 REMARK REVDAT 4 24-JUL-19 2UYC 1 REMARK LINK REVDAT 3 24-JAN-18 2UYC 1 SOURCE REVDAT 2 24-FEB-09 2UYC 1 VERSN REVDAT 1 27-MAY-08 2UYC 0 JRNL AUTH D.DAUJOTYTE,S.GRAZULIS JRNL TITL HHAI DNA METHYLTRANSFERASE R163N MUTANT COMPLEX WITH 13MER JRNL TITL 2 GCGC-GMGC OLIGONUCLEOTIDE AND SAH JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 32293104.370 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 36937 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) : 0.200 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3722 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5299 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 555 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2603 REMARK 3 NUCLEIC ACID ATOMS : 511 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.92000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 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) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.040 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) : 0.690 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.140 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.940 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.570 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 45.51 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 : SAH.PAR REMARK 3 PARAMETER FILE 7 : SO4.PAR REMARK 3 PARAMETER FILE 8 : GOL.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 : SAH.TOP REMARK 3 TOPOLOGY FILE 7 : SO4.TOP REMARK 3 TOPOLOGY FILE 8 : GOL.TOP REMARK 3 TOPOLOGY FILE 9 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESOLUTION-DEPENDENT WEIGHTING SCHEME REMARK 3 USED OTHER REFINEMENT REMARKS BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2UYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-APR-07. REMARK 100 THE DEPOSITION ID IS D_1290032189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : 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) : 0.8063 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 : 36938 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 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: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CITRATE PH 5.6, 1.8 M REMARK 280 AMMONIUM SULFATE, 5% GLUCOSE 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 47.49500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.42125 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 104.30100 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.49500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.42125 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 104.30100 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.49500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.42125 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 104.30100 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.49500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.42125 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 104.30100 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.49500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.42125 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 104.30100 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.49500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.42125 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 104.30100 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 54.84250 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 208.60200 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 54.84250 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 208.60200 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 54.84250 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 208.60200 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 54.84250 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 208.60200 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 54.84250 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 208.60200 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 54.84250 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 208.60200 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: REMARK: BASED ON PREVIOUS STRUCTURES OF HHAI REMARK 300 METHYLTRANSFERASEAND BIOCHEMICAL EXPERIMENTS, THE REMARK 300 TERNARY COMPLEX HHAIMETHYLTRANSFERASE-DNA-SAH IS REMARK 300 MONOMERIC 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: 7290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.3 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 A2116 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 163 TO ASN 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 2034 O HOH A 2035 2.05 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 D 422 P DG D 422 OP3 -0.084 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 37 143.50 -173.06 REMARK 500 ASP A 60 101.74 -1.99 REMARK 500 ALA A 77 104.00 -160.68 REMARK 500 ASP A 144 40.07 76.25 REMARK 500 ASN A 163 109.59 -40.96 REMARK 500 PHE A 259 42.35 -109.62 REMARK 500 LYS A 261 -6.28 63.13 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 SAH A1328 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1329 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1330 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1331 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1333 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1335 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1336 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1338 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1339 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: 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 REMARK 900 RELATED ID: 2C7R RELATED DB: PDB REMARK 900 HHAI DNA METHYLTRANSFERASE (T250G MUTANT) COMPLEX WITH REMARK 900 OLIGONUCLEOTIDE CONTAINING 2- AMINOPURINE AS A TARGET BASE (GPGC: REMARK 900 GMGC) AND SAH 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 999 REMARK 999 SEQUENCE REMARK 999 MUTATION R163N DBREF 2UYC A 1 327 UNP P05102 MTH1_HAEPH 1 327 DBREF 2UYC C 401 413 PDB 2UYC 2UYC 401 413 DBREF 2UYC D 422 433 PDB 2UYC 2UYC 422 433 SEQADV 2UYC ASN A 163 UNP P05102 ARG 163 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 ASN 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 DA DT DG 5CM DG DC DT DG DA DC SEQRES 1 D 12 DG DT DC DA DG DC DG DC DA DT DC DC MODRES 2UYC 5CM C 407 DC HET 5CM C 407 20 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 GOL A1335 6 HET GOL A1336 6 HET GOL A1337 6 HET GOL A1338 6 HET GOL A1339 6 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 SO4 6(O4 S 2-) FORMUL 11 GOL 5(C3 H8 O3) FORMUL 16 HOH *234(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 TYR A 157 5 3 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 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 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 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 SITE 1 AC1 23 PHE A 18 ALA A 19 LEU A 21 GLY A 23 SITE 2 AC1 23 ASN A 39 GLU A 40 TRP A 41 ASP A 42 SITE 3 AC1 23 ASP A 60 ILE A 61 GLY A 78 PRO A 80 SITE 4 AC1 23 TYR A 285 ASN A 304 SER A 305 VAL A 306 SITE 5 AC1 23 HOH A2192 HOH A2193 HOH A2204 HOH A2205 SITE 6 AC1 23 HOH A2206 HOH A2207 HOH A2208 SITE 1 AC2 3 PRO A 198 ASP A 199 HOH A2209 SITE 1 AC3 4 PRO A 286 ASP A 287 SER A 288 HOH A2181 SITE 1 AC4 4 LYS A 193 ARG A 245 LYS A 290 HOH A2126 SITE 1 AC5 4 LYS A 114 ARG A 172 HOH A2077 HOH A2211 SITE 1 AC6 4 ILE A 219 GLU A 220 GLN A 221 HOH A2212 SITE 1 AC7 3 ASN A 216 GLN A 217 HOH A2213 SITE 1 AC8 8 VAL A 151 LEU A 152 ASN A 153 ASP A 156 SITE 2 AC8 8 TYR A 157 PRO A 185 HOH A2098 HOH A2119 SITE 1 AC9 7 GLU A 3 ILE A 4 LYS A 5 ASP A 6 SITE 2 AC9 7 TYR A 316 TYR A 327 GOL A1337 SITE 1 BC1 5 TYR A 316 LYS A 325 PRO A 326 TYR A 327 SITE 2 BC1 5 GOL A1336 SITE 1 BC2 7 LYS A 261 LYS A 273 SER A 296 HOH A2166 SITE 2 BC2 7 DA C 404 DT C 405 HOH C2005 SITE 1 BC3 6 ASP A 199 SER A 200 GLU A 203 HIS A 275 SITE 2 BC3 6 HOH A2214 HOH A2215 CRYST1 94.990 94.990 312.903 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 0.010527 0.006078 0.000000 0.00000 SCALE2 0.000000 0.012156 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003196 0.00000