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- PDB-5maw: Crystal structure of the flagellin-FliS complex from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 5maw
TitleCrystal structure of the flagellin-FliS complex from Bacillus subtilis
Components
  • Flagellar protein FliS
  • Flagellin
KeywordsCHAPERONE / flagellum / type-3-secretion
Function / homology
Function and homology information


bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / cytosol
Similarity search - Function
Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region ...Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellin / Flagellar secretion chaperone FliS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAltegoer, F. / Bange, G.
CitationJournal: Sci Rep / Year: 2018
Title: FliS/flagellin/FliW heterotrimer couples type III secretion and flagellin homeostasis.
Authors: Altegoer, F. / Mukherjee, S. / Steinchen, W. / Bedrunka, P. / Linne, U. / Kearns, D.B. / Bange, G.
History
DepositionNov 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
D: Flagellin
E: Flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)48,6912
Polymers48,6912
Non-polymers00
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-32 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.138, 62.353, 65.078
Angle α, β, γ (deg.)90.00, 111.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flagellin


Mass: 33545.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hag, BSU35360 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02968
#2: Protein Flagellar protein FliS


Mass: 15146.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: fliS, BSU35330 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39739
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 7.0, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9723 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9723 Å / Relative weight: 1
ReflectionResolution: 1.5→48.57 Å / Num. obs: 61470 / % possible obs: 99 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04399 / Net I/σ(I): 18.17
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 6152 / CC1/2: 0.97 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IO1, 1VH6

1io1

1vh6


Resolution: 1.5→48.568 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 3021 4.92 %0.05
Rwork0.1729 ---
obs0.174 61439 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→48.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 0 359 3203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012879
X-RAY DIFFRACTIONf_angle_d0.9453888
X-RAY DIFFRACTIONf_dihedral_angle_d2.2992246
X-RAY DIFFRACTIONf_chiral_restr0.06454
X-RAY DIFFRACTIONf_plane_restr0.006523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52350.24281120.20932662X-RAY DIFFRACTION99
1.5235-1.54840.24331290.212662X-RAY DIFFRACTION99
1.5484-1.57510.22071310.20092669X-RAY DIFFRACTION99
1.5751-1.60380.23461250.19862688X-RAY DIFFRACTION99
1.6038-1.63460.25661480.1932627X-RAY DIFFRACTION99
1.6346-1.6680.2351240.1922638X-RAY DIFFRACTION98
1.668-1.70430.22021160.19732566X-RAY DIFFRACTION96
1.7043-1.74390.22181550.19922648X-RAY DIFFRACTION99
1.7439-1.78750.23561410.19422638X-RAY DIFFRACTION99
1.7875-1.83590.21331260.19522693X-RAY DIFFRACTION99
1.8359-1.88990.23971530.18442634X-RAY DIFFRACTION99
1.8899-1.95090.20531330.18442673X-RAY DIFFRACTION99
1.9509-2.02060.20061350.17952614X-RAY DIFFRACTION97
2.0206-2.10150.19661240.18392676X-RAY DIFFRACTION99
2.1015-2.19720.1811400.16812673X-RAY DIFFRACTION99
2.1972-2.3130.18381300.17482671X-RAY DIFFRACTION99
2.313-2.45790.19391250.17252666X-RAY DIFFRACTION99
2.4579-2.64770.21211350.17262647X-RAY DIFFRACTION98
2.6477-2.91410.19421760.16732652X-RAY DIFFRACTION99
2.9141-3.33570.17251290.16792673X-RAY DIFFRACTION99
3.3357-4.20220.18071600.15082641X-RAY DIFFRACTION98
4.2022-48.59340.17341740.16562707X-RAY DIFFRACTION98

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