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- PDB-1wlg: Crystal structure of FlgE31, a major fragment of the hook protein -

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Basic information

Entry
Database: PDB / ID: 1wlg
TitleCrystal structure of FlgE31, a major fragment of the hook protein
ComponentsFlagellar hook protein flgE
KeywordsSTRUCTURAL PROTEIN / EAR-& motif
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar hook protein FlgE / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein ...Flagellar hook protein FlgE / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsSamatey, F.A. / Matsunami, H. / Imada, K. / Nagashima, S. / Shaikh, T.R. / Thomas, D.R. / DeRosier, D.J. / Kitao, A. / Namba, K.
CitationJournal: Nature / Year: 2004
Title: Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism.
Authors: Fadel A Samatey / Hideyuki Matsunami / Katsumi Imada / Shigehiro Nagashima / Tanvir R Shaikh / Dennis R Thomas / James Z Chen / David J Derosier / Akio Kitao / Keiichi Namba /
Abstract: The bacterial flagellum is a motile organelle, and the flagellar hook is a short, highly curved tubular structure that connects the flagellar motor to the long filament acting as a helical propeller. ...The bacterial flagellum is a motile organelle, and the flagellar hook is a short, highly curved tubular structure that connects the flagellar motor to the long filament acting as a helical propeller. The hook is made of about 120 copies of a single protein, FlgE, and its function as a nano-sized universal joint is essential for dynamic and efficient bacterial motility and taxis. It transmits the motor torque to the helical propeller over a wide range of its orientation for swimming and tumbling. Here we report a partial atomic model of the hook obtained by X-ray crystallography of FlgE31, a major proteolytic fragment of FlgE lacking unfolded terminal regions, and by electron cryomicroscopy and three-dimensional helical image reconstruction of the hook. The model reveals the intricate molecular interactions and a plausible switching mechanism for the hook to be flexible in bending but rigid against twisting for its universal joint function.
History
DepositionJun 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar hook protein flgE
B: Flagellar hook protein flgE


Theoretical massNumber of molelcules
Total (without water)62,6702
Polymers62,6702
Non-polymers00
Water13,529751
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.714, 49.034, 96.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-666-

HOH

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Components

#1: Protein Flagellar hook protein flgE


Mass: 31335.084 Da / Num. of mol.: 2 / Fragment: FlgE31
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1J1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 2000, copper acetate, cacodylate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å
DetectorType: ADSC / Detector: CCD / Date: Jun 27, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection shellResolution: 1.8→1.846 Å / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.112 / SU ML: 0.095 / σ(F): 2 / ESU R: 0.138 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24153 2853 5.1 %RANDOM
Rwork0.19024 ---
all0.19285 71019 --
obs0.19285 53290 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.252 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--1.01 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 0 751 5063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214386
X-RAY DIFFRACTIONr_bond_other_d0.0020.023710
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9265986
X-RAY DIFFRACTIONr_angle_other_deg0.82838706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275584
X-RAY DIFFRACTIONr_chiral_restr0.0910.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025088
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02794
X-RAY DIFFRACTIONr_nbd_refined0.2250.2857
X-RAY DIFFRACTIONr_nbd_other0.2580.24469
X-RAY DIFFRACTIONr_nbtor_other0.0870.22657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2553
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3540.247
X-RAY DIFFRACTIONr_mcbond_it0.8961.52894
X-RAY DIFFRACTIONr_mcangle_it1.67224648
X-RAY DIFFRACTIONr_scbond_it2.51831492
X-RAY DIFFRACTIONr_scangle_it4.1254.51338
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 185
Rwork0.248 3573

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