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

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Basic information

Entry
Database: PDB / ID: 3rvp
TitleStructure of the CheY-BeF3 Complex with substitutions at 59 and 89: N59D and E89K
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / Response regulator / two-component / signal transduction / CheY / Beta-alpha protein / Chemotaxis / CheZ CheA 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 / 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
BERYLLIUM TRIFLUORIDE ION / : / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 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

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein CheY
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,67125
Polymers28,7912
Non-polymers1,88023
Water3,243180
1
A: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,38213
Polymers14,3961
Non-polymers98612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,29012
Polymers14,3961
Non-polymers89411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.487, 53.626, 160.416
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: 14395.659 Da / Num. of mol.: 2 / Mutation: N59D, E89K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1882, cheY, JW1871 / Plasmid: pET28aCheYN59DE89K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AE67

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Non-polymers , 6 types, 203 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.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 69.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium Sulfate 2.6M, Tris 100mM pH 7.5, Glycerol 5% (v/v), MnCl2 20mM, BeCl2 1mM, NaF 10mM, 4.6mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.00882 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2010 / Details: Sagittal crystal
RadiationMonochromator: Sagitally Focused Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00882 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 18724 / Num. obs: 18144 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 32.82 Å2 / Rsym value: 0.079 / Net I/σ(I): 22.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.57 / Num. unique all: 950 / Rsym value: 0.337 / % possible all: 70.7

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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 1FQW

1fqw


Resolution: 2.404→44.58 Å / SU ML: 0.31 / Isotropic thermal model: Individual / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 20.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1750 9.93 %R-free flag extended from Structure of CheY-BeF3 Complex with substitutions at 59 and 89: N59D and E89Q
Rwork0.1734 ---
obs0.1775 17615 94.2 %-
all-18699 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.346 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 32.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.036 Å20 Å2-0 Å2
2--2.2871 Å20 Å2
3----1.2511 Å2
Refinement stepCycle: LAST / Resolution: 2.404→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 108 180 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072141
X-RAY DIFFRACTIONf_angle_d1.0582867
X-RAY DIFFRACTIONf_dihedral_angle_d12.766806
X-RAY DIFFRACTIONf_chiral_restr0.065317
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4036-2.46860.3243900.2533829X-RAY DIFFRACTION65
2.4686-2.54120.30311160.25061027X-RAY DIFFRACTION80
2.5412-2.62330.30351250.24081151X-RAY DIFFRACTION91
2.6233-2.7170.26111330.21581215X-RAY DIFFRACTION95
2.717-2.82580.26381390.20271253X-RAY DIFFRACTION97
2.8258-2.95440.25061330.20081235X-RAY DIFFRACTION98
2.9544-3.11010.23711410.19991257X-RAY DIFFRACTION98
3.1101-3.30490.22131360.19391269X-RAY DIFFRACTION99
3.3049-3.55990.23491430.17211298X-RAY DIFFRACTION100
3.5599-3.9180.18461370.15481287X-RAY DIFFRACTION100
3.918-4.48450.17011490.12681327X-RAY DIFFRACTION100
4.4845-5.64820.16391500.13281309X-RAY DIFFRACTION100
5.6482-44.58760.20031580.1731408X-RAY DIFFRACTION100

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