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- PDB-1af7: CHER FROM SALMONELLA TYPHIMURIUM -

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Basic information

Entry
Database: PDB / ID: 1af7
TitleCHER FROM SALMONELLA TYPHIMURIUM
ComponentsCHEMOTAXIS RECEPTOR METHYLTRANSFERASE CHER
KeywordsMETHYLTRANSFERASE / CHEMOTAXIS RECEPTOR METHYLATION
Function / homology
Function and homology information


protein-glutamate O-methyltransferase / protein-glutamate O-methyltransferase activity / methyl accepting chemotaxis protein complex / protein methyltransferase activity / chemotaxis / methylation
Similarity search - Function
Chemotaxis Receptor Methyltransferase Cher; domain 1 / Chemotaxis receptor methyltransferase CheR, N-terminal domain / Chemotaxis protein methyltransferase CheR / MCP methyltransferase, CheR-type / Chemotaxis receptor methyltransferase CheR, N-terminal / MCP methyltransferase, CheR-type, SAM-binding domain, C-terminal / Chemotaxis receptor methyltransferase CheR, N-terminal domain superfamily / : / CheR methyltransferase, SAM binding domain / CheR methyltransferase, all-alpha domain ...Chemotaxis Receptor Methyltransferase Cher; domain 1 / Chemotaxis receptor methyltransferase CheR, N-terminal domain / Chemotaxis protein methyltransferase CheR / MCP methyltransferase, CheR-type / Chemotaxis receptor methyltransferase CheR, N-terminal / MCP methyltransferase, CheR-type, SAM-binding domain, C-terminal / Chemotaxis receptor methyltransferase CheR, N-terminal domain superfamily / : / CheR methyltransferase, SAM binding domain / CheR methyltransferase, all-alpha domain / CheR-type methyltransferase domain profile. / Methyltransferase, chemotaxis proteins / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Chemotaxis protein methyltransferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsDjordjevic, S. / Stock, A.M.
CitationJournal: Structure / Year: 1997
Title: Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine.
Authors: Djordjevic, S. / Stock, A.M.
History
DepositionMar 22, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHEMOTAXIS RECEPTOR METHYLTRANSFERASE CHER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9172
Polymers31,5331
Non-polymers3841
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.450, 47.960, 63.060
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHEMOTAXIS RECEPTOR METHYLTRANSFERASE CHER


Mass: 31533.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: STRUCTURE INCLUDES S-ADENOSYL-L-HOMOCYSTEINE / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PME43 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P07801, protein-glutamate O-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.6
Details: MICROSEEDING; 1.2 M AMMONIUM SULFATE, 2% PEG 400, 25 MM SODIUM CITRATE PH 5.6. PRIOR TO DATA COLLECTION CRYSTAL WAS SOAKED IN THE SAME SOLUTION WITH PH ADJUSTED TO 7.0.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.2 Mammonium salfate1reservoir
22 %PEG4001reservoir
325 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→34.3 Å / Num. obs: 18331 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 11
Reflection shellResolution: 2.06→2.25 Å / Redundancy: 2 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 6.4 / % possible all: 91.8

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Processing

Software
NameClassification
ARP/wARPmodel building
PHASESphasing
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MIR / Resolution: 2→34.3 Å / σ(F): 2
Details: RESIDUES 13 - 22, AND 184 - 194 BELONG TO WEAKLY DEFINED REGIONS. RESIDUE SER 125 HAS PHI PSI VALUES OUTSIDE OF THE EXPECTED RANGE BUT THIS IS REAL BUT THIS IS REAL AND IT IS TRUE FOR ALL ...Details: RESIDUES 13 - 22, AND 184 - 194 BELONG TO WEAKLY DEFINED REGIONS. RESIDUE SER 125 HAS PHI PSI VALUES OUTSIDE OF THE EXPECTED RANGE BUT THIS IS REAL BUT THIS IS REAL AND IT IS TRUE FOR ALL METHYLTRANSFERASES IN THAT POSITION. THAT RESIDUE IS PART OF THE LOOP THAT IS FOUND TO BE IMPORTANT FOR THE CATALYTIC PART OF THE LOOP THAT IS FOUND TO BE IMPORTANT FOR THE CATALYTIC ACTIVITY AND UNIQUE FOR METHYLTRANSFERASES. BACKBONE ANGLES FOR REGION 121 - 127 ARE ALSO DEVIATING BUT THEY TOO ARE INVOLVED IN FORMATION OF THIS SPECIFIC LOOP.
RfactorNum. reflection% reflection
Rfree0.28 -5 %
Rwork0.2 --
obs-18035 93 %
Refinement stepCycle: LAST / Resolution: 2→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 26 111 2401
Software
*PLUS
Name: ARP / Classification: refinement
Refinement
*PLUS
Num. reflection all: 18331 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.7

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