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- PDB-4hyn: X-ray crystal structure of Thermotoga maritima FliY -

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Basic information

Entry
Database: PDB / ID: 4hyn
TitleX-ray crystal structure of Thermotoga maritima FliY
ComponentsCheC, inhibitor of MCP methylation / FliN fusion protein
KeywordsSIGNALING PROTEIN / CheC like domain / Phosphatase
Function / homology
Function and homology information


bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
CheC-like protein / CheC-like family / CheC-like / Chemotaxis protein chec / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term ...CheC-like protein / CheC-like family / CheC-like / Chemotaxis protein chec / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsCrane, B.R. / Sircar, R. / Bilwes, A.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure and Activity of the Flagellar Rotor Protein FliY: A MEMBER OF THE CheC PHOSPHATASE FAMILY.
Authors: Sircar, R. / Greenswag, A.R. / Bilwes, A.M. / Gonzalez-Bonet, G. / Crane, B.R.
History
DepositionNov 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CheC, inhibitor of MCP methylation / FliN fusion protein
B: CheC, inhibitor of MCP methylation / FliN fusion protein


Theoretical massNumber of molelcules
Total (without water)45,2362
Polymers45,2362
Non-polymers00
Water3,099172
1
A: CheC, inhibitor of MCP methylation / FliN fusion protein


Theoretical massNumber of molelcules
Total (without water)22,6181
Polymers22,6181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CheC, inhibitor of MCP methylation / FliN fusion protein


Theoretical massNumber of molelcules
Total (without water)22,6181
Polymers22,6181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.750, 85.890, 119.940
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 CheC, inhibitor of MCP methylation / FliN fusion protein


Mass: 22618.010 Da / Num. of mol.: 2 / Fragment: CheC like domain (residues 24-223)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: ThemaDRAFT_0622 / Plasmid: Pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4FDE4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 30% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2011 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 34326 / Num. obs: 33692

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / σ(F): 10000 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 -RANDOM
Rwork0.21 --
obs0.21 33692 -
all-34326 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 0 172 3217
LS refinement shellResolution: 2.5→2.54 Å / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21

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