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- PDB-3rvn: Structure of the CheY-BeF3 Complex with substitutions at 59 and 8... -

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Basic information

Entry
Database: PDB / ID: 3rvn
TitleStructure of the CheY-BeF3 Complex with substitutions at 59 and 89: N59D and E89Y
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / Response regulator / two-component / signal transduction / CheY / Beta-alpha protein / Chemotaxis / CheA CheZ CheX / Phosphorylation
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
BERYLLIUM TRIFLUORIDE ION / : / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsStarbird, C.A. / Immormino, R.M. / Silversmith, R.E. / Bourret, R.B.
CitationJournal: Biochemistry / Year: 2015
Title: Probing Mechanistic Similarities between Response Regulator Signaling Proteins and Haloacid Dehalogenase Phosphatases.
Authors: Immormino, R.M. / Starbird, C.A. / Silversmith, R.E. / Bourret, R.B.
History
DepositionMay 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 protein CheY
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,22218
Polymers28,8592
Non-polymers1,36316
Water4,414245
1
A: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,29511
Polymers14,4301
Non-polymers86610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9277
Polymers14,4301
Non-polymers4976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.436, 53.613, 161.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chemotaxis protein CheY


Mass: 14429.653 Da / Num. of mol.: 2 / Mutation: N59D, E89Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1882, cheY, JW1871 / Plasmid: pET23aCheYN59DE89Y / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AE67

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Non-polymers , 5 types, 261 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: Ammonium Sulfate 2.0M Tris 100mM pH 8.25 Glycerol 5% (v/v) MnCl2 20mM BeCl2 1mM NaF 10mM CheY 8.9mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2011 / Details: Sagittal crystal
RadiationMonochromator: Sagitally Focused Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 22754 / Num. obs: 22709 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 32.24 Å2 / Rsym value: 0.125 / Net I/σ(I): 12.82
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1095 / Rsym value: 0.093 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FQW

1fqw


Resolution: 2.25→27.597 Å / SU ML: 0.26 / Isotropic thermal model: Individual / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1089 5.01 %R-free flag extended from Structure of CheY-BeF3 Complex with substitutions at 59 and 89: N59D and E89Q
Rwork0.1863 ---
obs0.1883 21750 95.49 %-
all-22754 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.91 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 35.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.513 Å2-0 Å20 Å2
2---4.3487 Å2-0 Å2
3---2.8357 Å2
Refinement stepCycle: LAST / Resolution: 2.25→27.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 78 245 2319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072107
X-RAY DIFFRACTIONf_angle_d1.112826
X-RAY DIFFRACTIONf_dihedral_angle_d12.701786
X-RAY DIFFRACTIONf_chiral_restr0.069315
X-RAY DIFFRACTIONf_plane_restr0.004355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.249-2.35130.3041190.26632300X-RAY DIFFRACTION87
2.3513-2.47520.28541200.24472444X-RAY DIFFRACTION92
2.4752-2.63010.29761230.22932488X-RAY DIFFRACTION93
2.6301-2.8330.23851420.21982591X-RAY DIFFRACTION96
2.833-3.11770.27621350.21052610X-RAY DIFFRACTION98
3.1177-3.56810.23721540.19182673X-RAY DIFFRACTION99
3.5681-4.49230.17711500.14782708X-RAY DIFFRACTION99
4.4923-27.59940.18661460.15582847X-RAY DIFFRACTION99

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