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

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Basic information

Entry
Database: PDB / ID: 3rvm
TitleStructure of the CheY-Mn2+ Complex with substitutions at 59 and 89: N59D and E89R
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / Response regulator / two-component / signal transduction / CheY / Beta-alpha protein / Chemotaxis / CheA CheX CheZ / 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: 1.45 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4792
Polymers14,4241
Non-polymers551
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.328, 47.019, 53.349
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: 14423.673 Da / Num. of mol.: 1 / Mutation: N59D, E89R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1882, cheY, JW1871 / Plasmid: pET28aCheYN59DE89R / 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.: 223 / 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: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: PEG 8000 26%, Na Cacodylate 100mM pH 6.0, Calcium Acetate 120mM, Glycerol 10% (v/v), 4.25 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: 1.02631 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: 1.02631 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 20957 / Num. obs: 20182 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 9.29 Å2 / Rsym value: 0.042 / Net I/σ(I): 38.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 8.8 / Num. unique all: 1027 / Rsym value: 0.125 / % possible all: 71.7

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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: 1.45→23.51 Å / SU ML: 0.11 / Isotropic thermal model: Individual + TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 14.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1659 1001 5.02 %R-free flag extended from Structure of CheY-Mn2+ Complex with substitutions at 59 and 89: N59D and E89Q
Rwork0.1394 ---
obs0.1408 19960 95.41 %-
all-20920 --
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.737 Å2 / ksol: 0.448 e/Å3
Displacement parametersBiso mean: 13.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.5102 Å20 Å20 Å2
2--1.1215 Å2-0 Å2
3---0.3886 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 1 223 1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151068
X-RAY DIFFRACTIONf_angle_d1.661448
X-RAY DIFFRACTIONf_dihedral_angle_d12.431422
X-RAY DIFFRACTIONf_chiral_restr0.086164
X-RAY DIFFRACTIONf_plane_restr0.008188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4476-1.52390.18591020.15372147X-RAY DIFFRACTION76
1.5239-1.61940.18841490.1422684X-RAY DIFFRACTION96
1.6194-1.74440.16361410.14142755X-RAY DIFFRACTION99
1.7444-1.91980.17861580.13692782X-RAY DIFFRACTION99
1.9198-2.19750.16321420.13292810X-RAY DIFFRACTION100
2.1975-2.76790.16211550.13312862X-RAY DIFFRACTION100
2.7679-23.51260.15751540.14412919X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.1328 Å / Origin y: 15.7336 Å / Origin z: 10.9323 Å
111213212223313233
T0.03 Å20.001 Å20.0029 Å2-0.0317 Å2-0.0045 Å2--0.0301 Å2
L0.5238 °20.1895 °20.3727 °2-0.3561 °2-0.02 °2--0.7478 °2
S0.0076 Å °-0.0362 Å °0.034 Å °0.0093 Å °-0.0005 Å °0.0146 Å °-0.0072 Å °-0.0476 Å °0.0004 Å °
Refinement TLS groupSelection details: chain a

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