HEADER TRANSFERASE (METHYLTRANSFERASE) 08-FEB-99 2HMY TITLE BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH ADOMET FORMED IN THE TITLE 2 PRESENCE OF A SHORT NONPSECIFIC DNA OLIGONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI); COMPND 3 CHAIN: B; COMPND 4 EC: 2.1.1.73; COMPND 5 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 KEYWDS TRANSFERASE (METHYLTRANSFERASE) EXPDTA X-RAY DIFFRACTION AUTHOR M.O'GARA,X.ZHANG,R.J.ROBERTS,X.CHENG REVDAT 5 30-AUG-23 2HMY 1 REMARK REVDAT 4 06-NOV-19 2HMY 1 JRNL REVDAT 3 24-FEB-09 2HMY 1 VERSN REVDAT 2 01-APR-03 2HMY 1 JRNL REVDAT 1 19-MAR-99 2HMY 0 JRNL AUTH M.O'GARA,X.ZHANG,R.J.ROBERTS,X.CHENG JRNL TITL STRUCTURE OF A BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH JRNL TITL 2 S-ADENOSYL-L-METHIONINE FORMED IN THE PRESENCE OF A SHORT JRNL TITL 3 NON-SPECIFIC DNA OLIGONUCLEOTIDE. JRNL REF J.MOL.BIOL. V. 287 201 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10080885 JRNL DOI 10.1006/JMBI.1999.2608 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.CHENG,S.KUMAR,J.POSFAI,J.W.PFLUGRATH,R.J.ROBERTS REMARK 1 TITL CRYSTAL STRUCTURE OF THE HHAI DNA METHYLTRANSFERASE REMARK 1 TITL 2 COMPLEXED WITH S-ADENOSYL-L-METHIONINE. REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 74 299 1993 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 8343957 REMARK 1 DOI 10.1016/0092-8674(93)90421-L REMARK 1 REFERENCE 2 REMARK 1 AUTH S.KUMAR,X.CHENG,J.W.PFLUGRATH,R.J.ROBERTS REMARK 1 TITL PURIFICATION, CRYSTALLIZATION, AND PRELIMINARY X-RAY REMARK 1 TITL 2 DIFFRACTION ANALYSIS OF AN M.HHAI-ADOMET COMPLEX. REMARK 1 REF BIOCHEMISTRY V. 31 8648 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 1390649 REMARK 1 DOI 10.1021/BI00151A035 REMARK 2 REMARK 2 RESOLUTION. 2.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 20104 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2104 REMARK 3 BIN R VALUE (WORKING SET) : 0.2945 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2606 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.790 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.88 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.650 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20104 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.610 REMARK 200 RESOLUTION RANGE LOW (A) : 34.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 1HMY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE 50 MMSODIUM REMARK 280 CITRATE PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 37.34000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 PRO B 70 150.29 -39.92 REMARK 500 LYS B 89 91.29 -56.32 REMARK 500 GLN B 90 -121.53 46.53 REMARK 500 ASP B 95 13.46 -69.71 REMARK 500 LYS B 112 75.26 40.74 REMARK 500 ASN B 123 40.80 -95.54 REMARK 500 ASP B 144 55.18 73.97 REMARK 500 ARG B 163 96.24 -172.37 REMARK 500 HIS B 204 22.51 -67.64 REMARK 500 PRO B 224 39.85 -95.06 REMARK 500 THR B 250 109.57 -58.11 REMARK 500 ALA B 260 -97.03 -26.09 REMARK 500 ASP B 287 -8.61 -57.13 REMARK 500 SER B 305 -158.01 -68.94 REMARK 500 SER B 320 -77.22 -53.64 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 SAM B 328 DBREF 2HMY B 1 327 UNP P05102 MTH1_HAEHA 1 327 SEQRES 1 B 327 MET ILE GLU ILE LYS ASP LYS GLN LEU THR GLY LEU ARG SEQRES 2 B 327 PHE ILE ASP LEU PHE ALA GLY LEU GLY GLY PHE ARG LEU SEQRES 3 B 327 ALA LEU GLU SER CYS GLY ALA GLU CYS VAL TYR SER ASN SEQRES 4 B 327 GLU TRP ASP LYS TYR ALA GLN GLU VAL TYR GLU MET ASN SEQRES 5 B 327 PHE GLY GLU LYS PRO GLU GLY ASP ILE THR GLN VAL ASN SEQRES 6 B 327 GLU LYS THR ILE PRO ASP HIS ASP ILE LEU CYS ALA GLY SEQRES 7 B 327 PHE PRO CYS GLN ALA PHE SER ILE SER GLY LYS GLN LYS SEQRES 8 B 327 GLY PHE GLU ASP SER ARG GLY THR LEU PHE PHE ASP ILE SEQRES 9 B 327 ALA ARG ILE VAL ARG GLU LYS LYS PRO LYS VAL VAL PHE SEQRES 10 B 327 MET GLU ASN VAL LYS ASN PHE ALA SER HIS ASP ASN GLY SEQRES 11 B 327 ASN THR LEU GLU VAL VAL LYS ASN THR MET ASN GLU LEU SEQRES 12 B 327 ASP TYR SER PHE HIS ALA LYS VAL LEU ASN ALA LEU ASP SEQRES 13 B 327 TYR GLY ILE PRO GLN LYS ARG GLU ARG ILE TYR MET ILE SEQRES 14 B 327 CYS PHE ARG ASN ASP LEU ASN ILE GLN ASN PHE GLN PHE SEQRES 15 B 327 PRO LYS PRO PHE GLU LEU ASN THR PHE VAL LYS ASP LEU SEQRES 16 B 327 LEU LEU PRO ASP SER GLU VAL GLU HIS LEU VAL ILE ASP SEQRES 17 B 327 ARG LYS ASP LEU VAL MET THR ASN GLN GLU ILE GLU GLN SEQRES 18 B 327 THR THR PRO LYS THR VAL ARG LEU GLY ILE VAL GLY LYS SEQRES 19 B 327 GLY GLY GLN GLY GLU ARG ILE TYR SER THR ARG GLY ILE SEQRES 20 B 327 ALA ILE THR LEU SER ALA TYR GLY GLY GLY ILE PHE ALA SEQRES 21 B 327 LYS THR GLY GLY TYR LEU VAL ASN GLY LYS THR ARG LYS SEQRES 22 B 327 LEU HIS PRO ARG GLU CYS ALA ARG VAL MET GLY TYR PRO SEQRES 23 B 327 ASP SER TYR LYS VAL HIS PRO SER THR SER GLN ALA TYR SEQRES 24 B 327 LYS GLN PHE GLY ASN SER VAL VAL ILE ASN VAL LEU GLN SEQRES 25 B 327 TYR ILE ALA TYR ASN ILE GLY SER SER LEU ASN PHE LYS SEQRES 26 B 327 PRO TYR HET SAM B 328 27 HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 HOH *63(H2 O) HELIX 1 1 GLY B 23 CYS B 31 1 9 HELIX 2 2 LYS B 43 ASN B 52 1 10 HELIX 3 3 ILE B 61 GLN B 63 5 3 HELIX 4 4 GLU B 66 THR B 68 5 3 HELIX 5 5 PHE B 93 SER B 96 5 4 HELIX 6 6 PHE B 101 LYS B 111 1 11 HELIX 7 7 LYS B 122 PHE B 124 5 3 HELIX 8 8 HIS B 127 LEU B 143 5 17 HELIX 9 9 ALA B 154 ASP B 156 5 3 HELIX 10 10 ASN B 173 LEU B 175 5 3 HELIX 11 11 VAL B 192 ASP B 194 5 3 HELIX 12 12 ASP B 199 LEU B 205 5 7 HELIX 13 13 PRO B 276 MET B 283 1 8 HELIX 14 14 THR B 295 ASN B 304 1 10 HELIX 15 15 ILE B 308 ASN B 323 1 16 SHEET 1 A 6 HIS B 148 ASN B 153 0 SHEET 2 A 6 GLU B 164 PHE B 171 -1 N ILE B 169 O HIS B 148 SHEET 3 A 6 VAL B 115 VAL B 121 -1 N ASN B 120 O ILE B 166 SHEET 4 A 6 ILE B 74 ALA B 77 1 N LEU B 75 O VAL B 115 SHEET 5 A 6 ARG B 13 LEU B 17 1 N ILE B 15 O ILE B 74 SHEET 6 A 6 GLU B 34 ASN B 39 1 N GLU B 34 O PHE B 14 SHEET 1 B 2 GLY B 264 VAL B 267 0 SHEET 2 B 2 LYS B 270 LYS B 273 -1 N ARG B 272 O TYR B 265 SHEET 1 C 2 ARG B 228 ILE B 231 0 SHEET 2 C 2 ARG B 240 TYR B 242 -1 N ILE B 241 O LEU B 229 SITE 1 AC1 17 PHE B 18 ALA B 19 GLY B 20 LEU B 21 SITE 2 AC1 17 GLY B 23 ASN B 39 GLU B 40 TRP B 41 SITE 3 AC1 17 ASP B 60 ILE B 61 GLY B 78 LEU B 100 SITE 4 AC1 17 TYR B 285 ASN B 304 SER B 305 VAL B 306 SITE 5 AC1 17 HOH B 376 CRYST1 55.300 74.680 90.960 90.00 103.00 90.00 P 1 21 1 2 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 0.018083 0.000000 0.004175 0.00000 SCALE2 0.000000 0.013390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011283 0.00000 MTRIX1 1 -0.502500 -0.840600 -0.202100 17.69330 1 MTRIX2 1 -0.841900 0.422600 0.335700 -10.04610 1 MTRIX3 1 -0.196800 0.338900 -0.920000 86.34150 1