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- PDB-3rvr: Structure of the CheYN59D/E89R Molybdate complex -

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Basic information

Entry
Database: PDB / ID: 3rvr
TitleStructure of the CheYN59D/E89R Molybdate complex
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 / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / 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 / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / 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
: / MOLYBDATE ION / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,79422
Polymers28,8472
Non-polymers1,94720
Water5,188288
1
A: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,29910
Polymers14,4241
Non-polymers8759
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,49512
Polymers14,4241
Non-polymers1,07211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.510, 53.630, 161.840
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: 14423.673 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 308 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-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: MoO4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 4.02 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.45 M Ammonium Sulfate, 100 mM Tris, pH 7.5, 5% (v/v) Glycerol, 2 mM Ammonium Molybdate, 20mM Manganese chloride, 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
RadiationMonochromator: sagital crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02631 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 28023 / Num. obs: 27965 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 34.63 Å2 / Rsym value: 0.061 / Net I/σ(I): 20.2
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 5.33 / Num. unique all: 2038 / Rsym value: 0.282 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CHY

3chy


Resolution: 2.1→19.735 Å / SU ML: 0.22 / Isotropic thermal model: individual / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 16.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 1481 5.34 %random extended from PDBID ???
Rwork0.1709 ---
obs0.1717 27715 99.07 %-
all-27975 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.312 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1-5.1486 Å2-0 Å2-0 Å2
2---2.5444 Å20 Å2
3----2.6042 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 97 288 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112116
X-RAY DIFFRACTIONf_angle_d1.2882850
X-RAY DIFFRACTIONf_dihedral_angle_d12.519781
X-RAY DIFFRACTIONf_chiral_restr0.078316
X-RAY DIFFRACTIONf_plane_restr0.006356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.16780.22541310.20972278X-RAY DIFFRACTION96
2.1678-2.24520.24461340.19942288X-RAY DIFFRACTION97
2.2452-2.33490.24411300.19342340X-RAY DIFFRACTION98
2.3349-2.4410.21111390.1872356X-RAY DIFFRACTION99
2.441-2.56940.19121310.18512341X-RAY DIFFRACTION99
2.5694-2.730.23771350.18912377X-RAY DIFFRACTION100
2.73-2.94020.20181330.18772396X-RAY DIFFRACTION100
2.9402-3.23490.19161360.18622394X-RAY DIFFRACTION100
3.2349-3.70030.15271300.15782423X-RAY DIFFRACTION100
3.7003-4.65190.16171360.13742464X-RAY DIFFRACTION100
4.6519-19.73540.16911460.16472577X-RAY DIFFRACTION100

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