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- PDB-1e6l: Two-component signal transduction system D13A mutant of CheY -

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Basic information

Entry
Database: PDB / ID: 1e6l
TitleTwo-component signal transduction system D13A mutant of CheY
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / TWO-COMPONENT SIGNAL TRANSDUCTION SYSTEM / CHEMOTAXIS / ACTIVE SITE MUTANT
Function / homology
Function and homology information


bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytoplasm / cytosol
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSola, M. / Lopez-Hernandez, E. / Cronet, P. / Lacroix, E. / Serrano, L. / Coll, M. / Parraga, A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the signal transduction protein CheY.
Authors: Sola, M. / Lopez-Hernandez, E. / Cronet, P. / Lacroix, E. / Serrano, L. / Coll, M. / Parraga, A.
History
DepositionAug 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / reflns / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_mutation / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _reflns.pdbx_Rsym_value / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein CheY


Theoretical massNumber of molelcules
Total (without water)13,8661
Polymers13,8661
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.100, 49.400, 53.700
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 protein CheY


Mass: 13866.049 Da / Num. of mol.: 1 / Mutation: D13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cheY, b1882, JW1871 / Plasmid: VECTOR DERIVED FROM PTZ 18 U / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P0AE67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION ASP13ALA TRANSMISSION OF SENSORY SIGNALS FROM THE CHEMORECEPTORS TO THE ...CHAIN A ENGINEERED MUTATION ASP13ALA TRANSMISSION OF SENSORY SIGNALS FROM THE CHEMORECEPTORS TO THE FLAGELLAR MOTORS.

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.25 mg/mlprotein1drop
212.5 %PEG80001drop
350 mMcacodylate1drop
425 %PEG80001reservoir
5100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 8137 / % possible obs: 88.7 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rsym value: 0.051
Reflection
*PLUS
Num. measured all: 36617 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.94 Å / % possible obs: 84.5 %

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Processing

SoftwareName: X-PLOR / Version: 3.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 --RANDOM
Rwork0.19 ---
obs0.19 8137 88.72 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 0 45 1016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.496
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Version: 3.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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