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- PDB-6ahp: Structure of the 58-167 fragment of FliL -

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Basic information

Entry
Database: PDB / ID: 6ahp
TitleStructure of the 58-167 fragment of FliL
ComponentsFlagellar protein FliLFlagellum
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: 2.1 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar protein FliL
B: Flagellar protein FliL


Theoretical massNumber of molelcules
Total (without water)24,0592
Polymers24,0592
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-6 kcal/mol
Surface area11320 Å2
Unit cell
Length a, b, c (Å)104.201, 104.201, 40.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsAuthor determined biological unit: unknown.

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Components

#1: Protein Flagellar protein FliL / Flagellum


Mass: 12029.596 Da / Num. of mol.: 2 / Fragment: periplasmic core fragment, residues 58-167
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl pH 8.0, 22% (w/v) PEG-4000, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 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: 2.1→52.101 Å / Num. obs: 14756 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 11233 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A model built by the Robetta server

Resolution: 2.1→52.101 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.42
RfactorNum. reflection% reflection
Rfree0.2585 1468 9.96 %
Rwork0.2055 --
obs0.2107 14737 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.66 Å2 / Biso mean: 43.1319 Å2 / Biso min: 16.23 Å2
Refinement stepCycle: final / Resolution: 2.1→52.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 0 159 1852
Biso mean---45.24 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161717
X-RAY DIFFRACTIONf_angle_d1.5342330
X-RAY DIFFRACTIONf_chiral_restr0.107278
X-RAY DIFFRACTIONf_plane_restr0.018307
X-RAY DIFFRACTIONf_dihedral_angle_d12.9371063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.17510.31571490.24891306100
2.1751-2.26220.28771450.23841314100
2.2622-2.36520.29011480.22641318100
2.3652-2.48990.28271470.22241318100
2.4899-2.64590.30511500.23421312100
2.6459-2.85020.2861420.22921323100
2.8502-3.13690.271440.22171330100
3.1369-3.59080.23111490.19321332100
3.5908-4.52360.22441470.17831340100
4.5236-52.1010.25281470.1939137699

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