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- PDB-5az4: Crystal structure of a 79KDa fragment of FlgE, the hook protein f... -

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Basic information

Entry
Database: PDB / ID: 5az4
TitleCrystal structure of a 79KDa fragment of FlgE, the hook protein from Campylobacter jejuni
ComponentsFlagellar hook subunit protein
KeywordsMOTOR PROTEIN / Flagellum / Hook / Universal joint
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility
Similarity search - Function
Flagellar hook FlgE / Flagellin hook, IN motif / Flagellin hook IN motif / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein ...Flagellar hook FlgE / Flagellin hook, IN motif / Flagellin hook IN motif / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / 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
Similarity search - Domain/homology
: / Flagellar hook protein FlgE
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsSamatey, F.A. / Kido, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Okinawa Institute of Science and Technology Japan
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights into bacterial flagellar hooks similarities and specificities.
Authors: Yoon, Y.-H. / Barker, C.S. / Bulieris, P.V. / Matsunami, H. / Samatey, F.A.
History
DepositionSep 25, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Flagellar hook subunit protein
B: Flagellar hook subunit protein
C: Flagellar hook subunit protein
D: Flagellar hook subunit protein


Theoretical massNumber of molelcules
Total (without water)314,6664
Polymers314,6664
Non-polymers00
Water26,4461468
1
A: Flagellar hook subunit protein


Theoretical massNumber of molelcules
Total (without water)78,6661
Polymers78,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagellar hook subunit protein


Theoretical massNumber of molelcules
Total (without water)78,6661
Polymers78,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flagellar hook subunit protein


Theoretical massNumber of molelcules
Total (without water)78,6661
Polymers78,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Flagellar hook subunit protein


Theoretical massNumber of molelcules
Total (without water)78,6661
Polymers78,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.457, 173.541, 147.086
Angle α, β, γ (deg.)90.00, 102.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Flagellar hook subunit protein / Flagellar hook protein FlgE


Mass: 78666.430 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 91-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: flgE_2, / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6GSW4, UniProt: Q0P7Q2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1468 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.2 M K2HPO4, 50 mM NaCl, 5 mM Tl2SO4, 12% DMSO, 50 mM MES pH 6.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9791, 0.9794
SYNCHROTRONSPring-8 BL41XU21
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDJan 20, 2011
RAYONIX MX225HE2CCDApr 22, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE-CRYSTALMADMx-ray1
2DOUBLE-CRYSTALSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
311
ReflectionResolution: 2.45→24.96 Å / Num. obs: 133379 / % possible obs: 98.39 % / Redundancy: 5.7 % / Net I/σ(I): 18.34

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(PHENIX.AUTOSOL: 1.7.1)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→24.956 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2287 8235 6.18 %
Rwork0.202 --
obs0.204 133258 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→24.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21712 0 0 1468 23180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422108
X-RAY DIFFRACTIONf_angle_d0.84430132
X-RAY DIFFRACTIONf_dihedral_angle_d11.9267776
X-RAY DIFFRACTIONf_chiral_restr0.0323392
X-RAY DIFFRACTIONf_plane_restr0.0034088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.49230.31083210.28175180X-RAY DIFFRACTION77
2.4923-2.53750.31214000.26646255X-RAY DIFFRACTION93
2.5375-2.58630.29313990.26036279X-RAY DIFFRACTION93
2.5863-2.6390.28844000.25516248X-RAY DIFFRACTION93
2.639-2.69640.29654090.24566294X-RAY DIFFRACTION93
2.6964-2.7590.28183880.23926246X-RAY DIFFRACTION93
2.759-2.82790.27234080.23816312X-RAY DIFFRACTION93
2.8279-2.90430.28984020.23456327X-RAY DIFFRACTION93
2.9043-2.98960.2584100.23246260X-RAY DIFFRACTION93
2.9896-3.08590.23713850.21986284X-RAY DIFFRACTION94
3.0859-3.1960.24214040.21846381X-RAY DIFFRACTION94
3.196-3.32370.24664190.20216308X-RAY DIFFRACTION93
3.3237-3.47460.23273960.20436285X-RAY DIFFRACTION94
3.4746-3.65720.21653980.19416354X-RAY DIFFRACTION94
3.6572-3.88550.22114050.18676325X-RAY DIFFRACTION94
3.8855-4.18430.20514100.17376380X-RAY DIFFRACTION94
4.1843-4.6030.18724050.16896329X-RAY DIFFRACTION94
4.603-5.26360.18244130.17416363X-RAY DIFFRACTION94
5.2636-6.6110.20363990.19456398X-RAY DIFFRACTION94
6.611-24.9470.22344160.19186459X-RAY DIFFRACTION94

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