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- PDB-3rvk: Structure of the CheY-Mn2+ Complex with substitutions at 59 and 8... -

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Basic information

Entry
Database: PDB / ID: 3rvk
TitleStructure of the CheY-Mn2+ Complex with substitutions at 59 and 89: N59D E89Q
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / two-component / signal transduction / response regulator / CheY / Beta-alpha protein / chemotaxis / CheZ / CheX / CheA / 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 / cytosol / cytoplasm
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsImmormino, R.M. / Starbird, C.A. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4502
Polymers14,3951
Non-polymers551
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.117, 46.786, 53.926
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: 14394.606 Da / Num. of mol.: 1 / Mutation: N59D, E89Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1882, cheY, JW1871 / Plasmid: pET28aCheYN59DE89Q / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AE67
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 1.98 Å3/Da / Density % sol: 37.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000 31% (w/v), Na Cacodylate 100mM, pH 6.0, Calcium Acetate 140mM, Glycerol 10% (v/v), 8.8 mg/mL CheY, 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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2010
RadiationMonochromator: sagital crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. all: 40217 / Num. obs: 39493 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 10.6 Å2 / Rsym value: 0.083 / Net I/σ(I): 19.1
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1963 / Rsym value: 0.399 / % possible all: 76.6

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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 3CHY

3chy


Resolution: 1.16→27.821 Å / SU ML: 0.14 / Isotropic thermal model: individual anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 13.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1589 1909 5.01 %random
Rwork0.1305 ---
obs0.1319 38086 94.79 %-
all-40179 --
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 90.208 Å2 / ksol: 0.501 e/Å3
Displacement parametersBiso mean: 16.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.5799 Å20 Å2-0 Å2
2--1.6675 Å20 Å2
3----1.0876 Å2
Refinement stepCycle: LAST / Resolution: 1.16→27.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 1 262 1250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071106
X-RAY DIFFRACTIONf_angle_d1.2161507
X-RAY DIFFRACTIONf_dihedral_angle_d11.992450
X-RAY DIFFRACTIONf_chiral_restr0.068169
X-RAY DIFFRACTIONf_plane_restr0.005198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1603-1.18930.3341930.27931900X-RAY DIFFRACTION71
1.1893-1.22140.27661470.24882283X-RAY DIFFRACTION86
1.2214-1.25740.24521180.19612476X-RAY DIFFRACTION91
1.2574-1.2980.19341610.16942519X-RAY DIFFRACTION95
1.298-1.34440.15991260.13772558X-RAY DIFFRACTION96
1.3444-1.39820.14821440.12372568X-RAY DIFFRACTION96
1.3982-1.46180.15221230.11982674X-RAY DIFFRACTION97
1.4618-1.53890.16151520.10892617X-RAY DIFFRACTION98
1.5389-1.63530.12051460.10692703X-RAY DIFFRACTION99
1.6353-1.76150.15651390.11152691X-RAY DIFFRACTION99
1.7615-1.93870.15561380.11312731X-RAY DIFFRACTION100
1.9387-2.21920.13991260.10832768X-RAY DIFFRACTION100
2.2192-2.79550.14061370.11642789X-RAY DIFFRACTION100
2.7955-27.82880.15621590.1412900X-RAY DIFFRACTION100

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