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- PDB-6ahq: Structure of the 40-167 fragment of FliL -

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Basic information

Entry
Database: PDB / ID: 6ahq
TitleStructure of the 40-167 fragment of FliL
ComponentsFlagellar protein FliL
KeywordsMOTOR PROTEIN / Flagellar motor protein
Function / homologyFlagellar basal body-associated protein FliL / Flagellar basal body-associated protein FliL / bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane / Flagellar protein FliL
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.398 Å
AuthorsTakekawa, N. / Isumi, M. / Sakuma, M. / Kojima, S. / Homma, M. / Imada, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP15H02386 Japan
Japan Society for the Promotion of ScienceJP16J01859 Japan
Japan Society for the Promotion of ScienceJP18K19293 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP23115008 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP24117004 Japan
CitationJournal: MBio / Year: 2019
Title: Structure ofVibrioFliL, a New Stomatin-like Protein That Assists the Bacterial Flagellar Motor Function.
Authors: Takekawa, N. / Isumi, M. / Terashima, H. / Zhu, S. / Nishino, Y. / Sakuma, M. / Kojima, S. / Homma, M. / Imada, K.
History
DepositionAug 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 protein FliL
B: Flagellar protein FliL
C: Flagellar protein FliL
D: Flagellar protein FliL
E: Flagellar protein FliL
F: Flagellar protein FliL
G: Flagellar protein FliL
H: Flagellar protein FliL
I: Flagellar protein FliL
J: Flagellar protein FliL
K: Flagellar protein FliL
L: Flagellar protein FliL
M: Flagellar protein FliL
N: Flagellar protein FliL
O: Flagellar protein FliL
P: Flagellar protein FliL
Q: Flagellar protein FliL
R: Flagellar protein FliL
S: Flagellar protein FliL
T: Flagellar protein FliL


Theoretical massNumber of molelcules
Total (without water)280,51420
Polymers280,51420
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33500 Å2
ΔGint-86 kcal/mol
Surface area87810 Å2
Unit cell
Length a, b, c (Å)162.139, 162.139, 302.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
DetailsAuthor determined biological unit: unknown.

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Components

#1: Protein
Flagellar protein FliL


Mass: 14025.714 Da / Num. of mol.: 20 / Fragment: periplasmic fragment, residues 60-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0P7ET86*PLUS

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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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate pH 6.0, 25 % (w/v) PEG-200, 0.15M CaCl2, 1.4% (v/v) EtOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.398→91.3 Å / Num. obs: 54933 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 51.07 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 10.8
Reflection shellResolution: 3.398→3.5 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 5 / Num. unique obs: 4467 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AHP

6ahp


Resolution: 3.398→85.551 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.23
RfactorNum. reflection% reflection
Rfree0.2449 2715 4.95 %
Rwork0.1867 --
obs0.1895 54840 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.82 Å2 / Biso mean: 54.6049 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 3.398→85.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16591 0 0 0 16591
Num. residues----2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216831
X-RAY DIFFRACTIONf_angle_d0.45222830
X-RAY DIFFRACTIONf_chiral_restr0.0412726
X-RAY DIFFRACTIONf_plane_restr0.0032993
X-RAY DIFFRACTIONf_dihedral_angle_d24.4736280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3984-3.46020.33851320.25572739287198
3.4602-3.52670.30081270.23652730285799
3.5267-3.59870.34511430.23872736287999
3.5987-3.6770.26551450.22062726287199
3.677-3.76250.27481500.20272743289399
3.7625-3.85660.29011520.20272701285398
3.8566-3.96090.27111310.212742287398
3.9609-4.07740.25331370.18282724286198
4.0774-4.2090.22811370.17572733287098
4.209-4.35950.2231430.15982734287798
4.3595-4.5340.20511510.152724287598
4.534-4.74030.19491320.15042764289698
4.7403-4.99020.20291520.14662731288398
4.9902-5.30290.22621490.162750289998
5.3029-5.71220.24451620.18312743290598
5.7122-6.28690.25861510.20272743289497
6.2869-7.19620.23991430.21532766290997
7.1962-9.06490.20421420.172748289094
9.0649-85.57810.22351360.18232848298492

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