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- PDB-1bc5: CHEMOTAXIS RECEPTOR RECOGNITION BY PROTEIN METHYLTRANSFERASE CHER -

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Basic information

Entry
Database: PDB / ID: 1bc5
TitleCHEMOTAXIS RECEPTOR RECOGNITION BY PROTEIN METHYLTRANSFERASE CHER
Components
  • CHEMOTAXIS RECEPTOR
  • CHEMOTAXIS RECEPTOR METHYLTRANSFERASE
KeywordsCOMPLEX (METHYLTRANSFERASE/PEPTIDE) / METHYLTRANSFERASE / PEPTIDE BINDING / CHEMOTAXIS RECEPTOR / COMPLEX (METHYLTRANSFERASE-PEPTIDE) / COMPLEX (METHYLTRANSFERASE-PEPTIDE) complex
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDjordjevic, S. / Stock, A.M.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Chemotaxis receptor recognition by protein methyltransferase CheR.
Authors: Djordjevic, S. / Stock, A.M.
History
DepositionMay 5, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHEMOTAXIS RECEPTOR METHYLTRANSFERASE
T: CHEMOTAXIS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1574
Polymers31,7142
Non-polymers4432
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-16 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.910, 70.580, 72.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHEMOTAXIS RECEPTOR METHYLTRANSFERASE / CHER / CHEMOTAXIS PROTEIN METHYLTRANSFERASE


Mass: 30992.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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: Protein/peptide CHEMOTAXIS RECEPTOR / TAR


Mass: 721.757 Da / Num. of mol.: 1
Fragment: C-TERMINAL PENTAPEPTIDE, ACETYLATED ASN-TRP-GLU-THR-PHE
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 52 %
Crystal growpH: 6.8
Details: PROTEIN WAS CRYSTALLIZED FROM 30 % PEG 5000 MME, 25 MM IMIDAZOLE PH 6.8, 15 MM COCL2, 1MM BETA-MERCAPTOETHANOL.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
20.1 Mimidazole1drop
315 mM1dropCoCl2
416 %mPEG50001drop
51 mMbeta-mercaptoethanol1drop
630 %mPEG50001reservoir
725 mMimidazole1reservoir
815 mM1reservoirCoCl2
91 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→23 Å / Num. obs: 16682 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.064 / Net I/σ(I): 7.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.28 / % possible all: 89
Reflection
*PLUS
Num. measured all: 52170 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AF7

1af7


Resolution: 2.2→8 Å / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.288 795 5 %RANDOM
Rwork0.204 ---
obs0.204 16017 86.7 %-
Displacement parametersBiso mean: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 27 121 2387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.204 / % reflection Rfree: 5 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.69
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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