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- PDB-3rvo: Structure of CheY-Mn2+ Complex with substitutions at 59 and 89: N... -

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Basic information

Entry
Database: PDB / ID: 3rvo
TitleStructure of CheY-Mn2+ Complex with substitutions at 59 and 89: N59D E89Y
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)14,4852
Polymers14,4301
Non-polymers551
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.364, 46.885, 53.524
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: 14429.653 Da / Num. of mol.: 1 / 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: pET28aCheYN59DE89Y / 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.: 174 / 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: 37.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000 30%, Na Cacodylate 100mM pH 6.0, Calcium Acetate 120mM, Glycerol 10% (v/v), 8.9 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: 0.97933 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2011
RadiationMonochromator: Sagital Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 17271 / Num. obs: 17012 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 13.18 Å2 / Rsym value: 0.086 / Net I/σ(I): 19.4
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 860 / Rsym value: 0.206 / % possible all: 97.8

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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: 1.55→23.442 Å / SU ML: 0.15 / Isotropic thermal model: Individual + TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 807 4.82 %R-free flag extended from Structure of CheY-Mn2+ Complex with substitutions at 59 and 89: N59D and E89Q
Rwork0.1521 ---
obs0.1537 16728 96.67 %-
all-17271 --
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.426 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1-2.771 Å2-0 Å2-0 Å2
2---1.7662 Å20 Å2
3----1.0048 Å2
Refinement stepCycle: LAST / Resolution: 1.55→23.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 1 174 1165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081106
X-RAY DIFFRACTIONf_angle_d1.1931506
X-RAY DIFFRACTIONf_dihedral_angle_d12.283444
X-RAY DIFFRACTIONf_chiral_restr0.069169
X-RAY DIFFRACTIONf_plane_restr0.005196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5452-1.6420.21531330.1712455X-RAY DIFFRACTION92
1.642-1.76870.18451340.16412628X-RAY DIFFRACTION97
1.7687-1.94670.19241270.14832678X-RAY DIFFRACTION98
1.9467-2.22820.1831270.1442707X-RAY DIFFRACTION99
2.2282-2.80650.16851360.14792710X-RAY DIFFRACTION98
2.8065-23.44520.18821500.15362743X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 14.1332 Å / Origin y: 15.9887 Å / Origin z: 10.9586 Å
111213212223313233
T0.0578 Å20.0021 Å20.0052 Å2-0.0634 Å2-0.0041 Å2--0.0613 Å2
L0.7857 °20.2446 °20.7398 °2-0.728 °20.0919 °2--1.1165 °2
S0.0023 Å °-0.0439 Å °0.0211 Å °0.0209 Å °0.0007 Å °0.0388 Å °0.0239 Å °-0.0705 Å °0.0078 Å °
Refinement TLS groupSelection details: chain a

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