PDB Short entry for 2UYH HEADER TRANSFERASE 06-APR-07 2UYH TITLE HHAI DNA METHYLTRANSFERASE S87Q-Q237S MUTANT COMPLEX WITH 13MER GCGC- TITLE 2 GMGC OLIGONUCLEOTIDE AND SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: MODIFICATION METHYLASE HHAI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HHAI DNA METHYLTRANSFERASE, CYTOSINE-SPECIFIC COMPND 5 METHYLTRANSFERASE HHAI, M.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(*TP*GP*GP*AP*TP*G*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 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES 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 4 13-DEC-23 2UYH 1 REMARK REVDAT 3 24-JUL-19 2UYH 1 REMARK LINK REVDAT 2 24-FEB-09 2UYH 1 VERSN REVDAT 1 27-MAY-08 2UYH 0 JRNL AUTH D.DAUJOTYTE,S.GRAZULIS JRNL TITL HHAI DNA METHYLTRANSFERASE S87Q-Q237S MUTANT COMPLEX WITH JRNL TITL 2 13MER GCGC-GMGC OLIGONUCLEOTIDE AND SAH JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.63 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) : 2.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 37849971.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16696 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 : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1728 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2414 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 295 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2606 REMARK 3 NUCLEIC ACID ATOMS : 511 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -2.06000 REMARK 3 B12 (A**2) : 5.83000 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.33 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.010 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) : 1.510 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.380 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.660 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.680 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 55.25 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 : 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESOLUTION-DEPENDENT WEIGHTING SCHEME REMARK 3 USED. BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2UYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-07. REMARK 100 THE DEPOSITION ID IS D_1290032161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-04 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) : 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 : 16740 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.630 REMARK 200 RESOLUTION RANGE LOW (A) : 34.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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 (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CITRATE PH 5.6, 1.6 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 47.69100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.53441 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 104.32400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.69100 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.53441 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 104.32400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.69100 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.53441 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 104.32400 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.69100 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.53441 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 104.32400 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.69100 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.53441 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 104.32400 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.69100 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.53441 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 104.32400 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 55.06882 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 208.64800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 55.06882 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 208.64800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 55.06882 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 208.64800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 55.06882 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 208.64800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 55.06882 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 208.64800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 55.06882 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 208.64800 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: 5720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.4 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, SER 87 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLN 237 TO SER 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 -0.083 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 16 79.48 -102.85 REMARK 500 ALA A 19 -54.11 -26.68 REMARK 500 GLU A 55 158.16 -45.10 REMARK 500 ASP A 60 107.32 -10.94 REMARK 500 PRO A 80 163.54 -46.70 REMARK 500 CYS A 81 -10.24 -143.49 REMARK 500 GLN A 90 36.97 39.86 REMARK 500 LYS A 112 68.47 28.36 REMARK 500 ASP A 144 49.05 74.03 REMARK 500 PRO A 160 76.42 -68.50 REMARK 500 LYS A 210 -16.80 -47.72 REMARK 500 MET A 214 102.20 -56.49 REMARK 500 PHE A 259 45.44 -102.54 REMARK 500 LYS A 261 -23.56 66.03 REMARK 500 ASN A 268 65.14 39.02 REMARK 500 SER A 305 -169.16 -72.13 REMARK 500 LEU A 322 -32.90 -35.89 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 DC D 433 0.06 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 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: 2UYC RELATED DB: PDB REMARK 900 HHAI DNA METHYLTRANSFERASE R163N MUTANT COMPLEX WITH 13MER GCGC- REMARK 900 GMGC OLIGONUCLEOTIDE AND SAH 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 MUTATIONS S87Q AND Q237S DBREF 2UYH A 1 327 UNP P05102 MTH1_HAEPH 1 327 DBREF 2UYH C 401 413 PDB 2UYH 2UYH 401 413 DBREF 2UYH D 422 433 PDB 2UYH 2UYH 422 433 SEQADV 2UYH GLN A 87 UNP P05102 SER 87 ENGINEERED MUTATION SEQADV 2UYH SER A 237 UNP P05102 GLN 237 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 GLN 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 SER 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 2UYH 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 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM SO4 SULFATE ION FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 SO4 4(O4 S 2-) FORMUL 9 HOH *89(H2 O) HELIX 1 1 GLY A 22 SER A 30 1 9 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 LYS A 91 ASP A 95 5 5 HELIX 5 5 LEU A 100 LYS A 112 1 13 HELIX 6 6 ASN A 123 ALA A 125 5 3 HELIX 7 7 SER A 126 LEU A 143 1 18 HELIX 8 8 LEU A 155 GLY A 158 5 4 HELIX 9 9 ASN A 173 ASN A 176 5 4 HELIX 10 10 PHE A 191 LEU A 195 5 5 HELIX 11 11 PRO A 198 VAL A 202 5 5 HELIX 12 12 HIS A 275 VAL A 282 1 8 HELIX 13 13 SER A 294 SER A 305 1 12 HELIX 14 14 VAL A 307 ASN A 323 1 17 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 ALA A 77 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 4 ARG A 228 ILE A 231 0 SHEET 2 AB 4 ARG A 240 SER A 243 -1 O ILE A 241 N LEU A 229 SHEET 3 AB 4 GLY A 264 VAL A 267 1 O GLY A 264 N TYR A 242 SHEET 4 AB 4 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 18 PHE A 18 ALA A 19 LEU A 21 GLY A 23 SITE 2 AC1 18 ASN A 39 GLU A 40 TRP A 41 ASP A 42 SITE 3 AC1 18 ASP A 60 ILE A 61 GLY A 78 ASN A 304 SITE 4 AC1 18 SER A 305 VAL A 306 HOH A2026 HOH A2068 SITE 5 AC1 18 HOH A2069 HOH A2077 SITE 1 AC2 4 PRO A 198 ASP A 199 HOH A2078 HOH A2079 SITE 1 AC3 3 PRO A 286 ASP A 287 SER A 288 SITE 1 AC4 3 LYS A 193 ARG A 245 LYS A 290 SITE 1 AC5 2 LYS A 114 ARG A 172 CRYST1 95.382 95.382 312.972 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 0.010484 0.006053 0.000000 0.00000 SCALE2 0.000000 0.012106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003195 0.00000