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- PDB-6jf2: Crystal structure of a 20kDa fragment of FlgG -

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Basic information

Entry
Database: PDB / ID: 6jf2
TitleCrystal structure of a 20kDa fragment of FlgG
ComponentsFlagellar basal-body rod protein FlgG
KeywordsSTRUCTURAL PROTEIN / Bacterial flagellum / distal rod
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar basal-body rod FlgG / 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
Similarity search - Domain/homology
Flagellar basal-body rod protein FlgG
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSaijo-Hamano, Y. / Matsunami, H. / Namba, K. / Imada, K.
CitationJournal: Biomolecules / Year: 2019
Title: Architecture of the Bacterial Flagellar Distal Rod and Hook of .
Authors: Yumiko Saijo-Hamano / Hideyuki Matsunami / Keiichi Namba / Katsumi Imada /
Abstract: The bacterial flagellum is a large molecular complex composed of thousands of protein subunits for motility. The filamentous part of the flagellum, which is called the axial structure, consists of ...The bacterial flagellum is a large molecular complex composed of thousands of protein subunits for motility. The filamentous part of the flagellum, which is called the axial structure, consists of the filament, the hook, and the rods, with other minor components-the cap protein and the hook associated proteins. They share a common basic architecture of subunit arrangement, but each part shows quite distinct mechanical properties to achieve its specific function. The distal rod and the hook are helical assemblies of a single protein, FlgG and FlgE, respectively. They show a significant sequence similarity but have distinct mechanical characteristics. The rod is a rigid, straight cylinder, whereas the hook is a curved tube with high bending flexibility. Here, we report a structural model of the rod constructed by using the crystal structure of a core fragment of FlgG with a density map obtained previously by electron cryomicroscopy. Our structural model suggests that a segment called L-stretch plays a key role in achieving the distinct mechanical properties of the rod using a structurally similar component protein to that of the hook.
History
DepositionFeb 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar basal-body rod protein FlgG
B: Flagellar basal-body rod protein FlgG


Theoretical massNumber of molelcules
Total (without water)38,7712
Polymers38,7712
Non-polymers00
Water3,459192
1
A: Flagellar basal-body rod protein FlgG


Theoretical massNumber of molelcules
Total (without water)19,3861
Polymers19,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar basal-body rod protein FlgG


Theoretical massNumber of molelcules
Total (without water)19,3861
Polymers19,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.530, 67.040, 110.270
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 Flagellar basal-body rod protein FlgG / FlgG / Distal rod protein


Mass: 19385.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: flgG, fla FVII, flaL, STM1179 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P0A1J3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 28-32% PEG monomethyl ether 2000, 0.1M acetate buffer (pH4.6), 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 1, 2011
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→36.8 Å / Num. obs: 24009 / % possible obs: 98.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4 / Num. unique obs: 3421 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.578 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.2287 1217 5.08 %
Rwork0.2001 --
obs0.2016 23964 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→36.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 0 192 2398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022301
X-RAY DIFFRACTIONf_angle_d0.5373142
X-RAY DIFFRACTIONf_dihedral_angle_d2.0631840
X-RAY DIFFRACTIONf_chiral_restr0.04365
X-RAY DIFFRACTIONf_plane_restr0.003431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.31831240.24762448X-RAY DIFFRACTION97
2.0801-2.17480.19181190.22562471X-RAY DIFFRACTION97
2.1748-2.28940.25241470.20242485X-RAY DIFFRACTION98
2.2894-2.43280.22941370.2072487X-RAY DIFFRACTION98
2.4328-2.62060.25681390.21262491X-RAY DIFFRACTION98
2.6206-2.88420.25031360.21192519X-RAY DIFFRACTION98
2.8842-3.30140.25011330.19962556X-RAY DIFFRACTION98
3.3014-4.15840.2111450.18762582X-RAY DIFFRACTION99
4.1584-36.58450.2011370.18752708X-RAY DIFFRACTION98

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