PDB Short entry for 1AF7 HEADER METHYLTRANSFERASE 22-MAR-97 1AF7 TITLE CHER FROM SALMONELLA TYPHIMURIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHEMOTAXIS RECEPTOR METHYLTRANSFERASE CHER; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.80; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: STRUCTURE INCLUDES S-ADENOSYL-L-HOMOCYSTEINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HB101; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PME43 KEYWDS METHYLTRANSFERASE, CHEMOTAXIS RECEPTOR METHYLATION EXPDTA X-RAY DIFFRACTION AUTHOR S.DJORDJEVIC,A.M.STOCK REVDAT 3 07-FEB-24 1AF7 1 REMARK REVDAT 2 24-FEB-09 1AF7 1 VERSN REVDAT 1 28-JAN-98 1AF7 0 JRNL AUTH S.DJORDJEVIC,A.M.STOCK JRNL TITL CRYSTAL STRUCTURE OF THE CHEMOTAXIS RECEPTOR JRNL TITL 2 METHYLTRANSFERASE CHER SUGGESTS A CONSERVED STRUCTURAL MOTIF JRNL TITL 3 FOR BINDING S-ADENOSYLMETHIONINE. JRNL REF STRUCTURE V. 5 545 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9115443 JRNL DOI 10.1016/S0969-2126(97)00210-4 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARP/WARP REMARK 3 AUTHORS : LAMZIN,PERRAKIS,MORRIS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 18035 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) : 0.200 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL 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 : 2224 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 111 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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: REMARK 3 RESIDUES 13 - 22, AND 184 - 194 BELONG TO WEAKLY DEFINED REMARK 3 REGIONS. RESIDUE SER 125 HAS PHI PSI VALUES OUTSIDE OF THE REMARK 3 EXPECTED RANGE BUT THIS IS REAL BUT THIS IS REAL AND IT IS REMARK 3 TRUE FOR ALL METHYLTRANSFERASES IN THAT POSITION. THAT REMARK 3 RESIDUE IS PART OF THE LOOP THAT IS FOUND TO BE IMPORTANT REMARK 3 FOR THE CATALYTIC PART OF THE LOOP THAT IS FOUND TO BE REMARK 3 IMPORTANT FOR THE CATALYTIC ACTIVITY AND UNIQUE FOR REMARK 3 METHYLTRANSFERASES. BACKBONE ANGLES FOR REGION 121 - 127 REMARK 3 ARE ALSO DEVIATING BUT THEY TOO ARE INVOLVED IN FORMATION REMARK 3 OF THIS SPECIFIC LOOP. REMARK 4 REMARK 4 1AF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-95 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18331 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 34.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.01300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MICROSEEDING; 1.2 M AMMONIUM SULFATE, REMARK 280 2% PEG 400, 25 MM SODIUM CITRATE PH 5.6. PRIOR TO DATA REMARK 280 COLLECTION CRYSTAL WAS SOAKED IN THE SAME SOLUTION WITH PH REMARK 280 ADJUSTED TO 7.0. 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 23.98000 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: A 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: 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 115 N - CA - C ANGL. DEV. = -15.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 13 85.96 -154.01 REMARK 500 GLN A 15 -96.88 -77.58 REMARK 500 MET A 16 112.49 74.69 REMARK 500 GLN A 77 -6.22 -55.50 REMARK 500 ARG A 112 -79.90 -81.01 REMARK 500 ARG A 113 90.40 -41.64 REMARK 500 SER A 125 -134.66 54.21 REMARK 500 VAL A 232 -37.04 -135.33 REMARK 500 GLN A 278 93.34 -58.80 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 A 287 DBREF 1AF7 A 11 284 UNP P07801 CHER_SALTY 11 284 SEQRES 1 A 274 SER VAL LEU LEU GLN MET THR GLN ARG LEU ALA LEU SER SEQRES 2 A 274 ASP ALA HIS PHE ARG ARG ILE CYS GLN LEU ILE TYR GLN SEQRES 3 A 274 ARG ALA GLY ILE VAL LEU ALA ASP HIS LYS ARG ASP MET SEQRES 4 A 274 VAL TYR ASN ARG LEU VAL ARG ARG LEU ARG ALA LEU GLY SEQRES 5 A 274 LEU ASP ASP PHE GLY ARG TYR LEU SER MET LEU GLU ALA SEQRES 6 A 274 ASN GLN ASN SER ALA GLU TRP GLN ALA PHE ILE ASN ALA SEQRES 7 A 274 LEU THR THR ASN LEU THR ALA PHE PHE ARG GLU ALA HIS SEQRES 8 A 274 HIS PHE PRO ILE LEU ALA GLU HIS ALA ARG ARG ARG HIS SEQRES 9 A 274 GLY GLU TYR ARG VAL TRP SER ALA ALA ALA SER THR GLY SEQRES 10 A 274 GLU GLU PRO TYR SER ILE ALA ILE THR LEU ALA ASP ALA SEQRES 11 A 274 LEU GLY MET ALA PRO GLY ARG TRP LYS VAL PHE ALA SER SEQRES 12 A 274 ASP ILE ASP THR GLU VAL LEU GLU LYS ALA ARG SER GLY SEQRES 13 A 274 ILE TYR ARG LEU SER GLU LEU LYS THR LEU SER PRO GLN SEQRES 14 A 274 GLN LEU GLN ARG TYR PHE MET ARG GLY THR GLY PRO HIS SEQRES 15 A 274 GLU GLY LEU VAL ARG VAL ARG GLN GLU LEU ALA ASN TYR SEQRES 16 A 274 VAL GLU PHE SER SER VAL ASN LEU LEU GLU LYS GLN TYR SEQRES 17 A 274 ASN VAL PRO GLY PRO PHE ASP ALA ILE PHE CYS ARG ASN SEQRES 18 A 274 VAL MET ILE TYR PHE ASP LYS THR THR GLN GLU ASP ILE SEQRES 19 A 274 LEU ARG ARG PHE VAL PRO LEU LEU LYS PRO ASP GLY LEU SEQRES 20 A 274 LEU PHE ALA GLY HIS SER GLU ASN PHE SER ASN LEU VAL SEQRES 21 A 274 ARG GLU PHE SER LEU ARG GLY GLN THR VAL TYR ALA LEU SEQRES 22 A 274 SER HET SAH A 287 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *111(H2 O) HELIX 1 1 ASP A 24 ALA A 38 1 15 HELIX 2 2 ASP A 44 LEU A 61 5 18 HELIX 3 3 PHE A 66 ALA A 75 1 10 HELIX 4 4 ALA A 80 LEU A 89 5 10 HELIX 5 5 ALA A 100 ARG A 112 5 13 HELIX 6 6 GLU A 128 ALA A 140 1 13 HELIX 7 7 THR A 157 SER A 165 1 9 HELIX 8 8 LEU A 170 LEU A 173 5 4 HELIX 9 9 PRO A 178 TYR A 184 1 7 HELIX 10 10 GLN A 200 TYR A 205 1 6 HELIX 11 11 MET A 233 TYR A 235 5 3 HELIX 12 12 LYS A 238 LEU A 251 1 14 SHEET 1 A 7 PHE A 273 GLY A 277 0 SHEET 2 A 7 VAL A 280 LEU A 283 -1 N ALA A 282 O SER A 274 SHEET 3 A 7 LEU A 257 ALA A 260 -1 N LEU A 258 O TYR A 281 SHEET 4 A 7 ALA A 226 CYS A 229 1 N ILE A 227 O LEU A 257 SHEET 5 A 7 TYR A 117 SER A 121 1 N TRP A 120 O ALA A 226 SHEET 6 A 7 TRP A 148 ASP A 154 1 N LYS A 149 O TYR A 117 SHEET 7 A 7 VAL A 206 SER A 210 1 N GLU A 207 O VAL A 150 SHEET 1 B 3 ILE A 167 ARG A 169 0 SHEET 2 B 3 LEU A 195 VAL A 198 -1 N VAL A 196 O TYR A 168 SHEET 3 B 3 PHE A 185 ARG A 187 -1 N MET A 186 O ARG A 197 CISPEP 1 GLY A 222 PRO A 223 0 0.17 SITE 1 AC1 17 ALA A 38 THR A 91 ASN A 92 THR A 94 SITE 2 AC1 17 ARG A 98 ALA A 123 GLU A 129 ASP A 154 SITE 3 AC1 17 ILE A 155 ASP A 156 VAL A 211 ASN A 212 SITE 4 AC1 17 LEU A 213 ARG A 230 ASN A 231 VAL A 232 SITE 5 AC1 17 PHE A 236 CRYST1 55.450 47.960 63.060 90.00 112.64 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 0.018034 0.000000 0.007522 0.00000 SCALE2 0.000000 0.020851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017182 0.00000