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- PDB-6gow: Crystal structure of the flagellin-FliS complex from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 6gow
TitleCrystal structure of the flagellin-FliS complex from Bacillus subtilis crystallized in spacegroup P22121
Components
  • Flagellar secretion chaperone 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
Flagellar secretion chaperone FliS / Flagellin / Flagellin / Flagellar secretion chaperone FliS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJun 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

Deposited unit
D: Flagellin
E: Flagellar secretion chaperone FliS


Theoretical massNumber of molelcules
Total (without water)47,8052
Polymers47,8052
Non-polymers00
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-33 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.860, 89.956, 116.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11D-553-

HOH

21D-645-

HOH

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Components

#1: Protein Flagellin


Mass: 32659.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3365 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A162QQD4, UniProt: P02968*PLUS
#2: Protein Flagellar secretion chaperone FliS


Mass: 15146.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3362, SC09_contig4orf00739 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A063XD95, UniProt: P39739*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Na-Cacodylate pH 6.5, 5% PEG 8000, 40 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→48.77 Å / Num. obs: 31628 / % possible obs: 99.29 % / Redundancy: 4.2 % / CC1/2: 0.995 / Rrim(I) all: 0.083 / Net I/σ(I): 13.65
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 4 % / Mean I/σ(I) obs: 7.17 / Num. unique obs: 3022 / CC1/2: 0.974 / Rrim(I) all: 0.1551 / % possible all: 97.61

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MAW

5maw


Resolution: 2.1→48.77 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.48
RfactorNum. reflection% reflection
Rfree0.2039 2000 6.32 %
Rwork0.1751 --
obs0.1769 31628 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 0 358 3150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032811
X-RAY DIFFRACTIONf_angle_d0.5133792
X-RAY DIFFRACTIONf_dihedral_angle_d5.1161744
X-RAY DIFFRACTIONf_chiral_restr0.035446
X-RAY DIFFRACTIONf_plane_restr0.002508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.24881370.18362020X-RAY DIFFRACTION97
2.1525-2.21070.2361390.17752083X-RAY DIFFRACTION100
2.2107-2.27580.21521420.17622088X-RAY DIFFRACTION100
2.2758-2.34920.18341420.16482106X-RAY DIFFRACTION100
2.3492-2.43320.17021410.16962088X-RAY DIFFRACTION99
2.4332-2.53060.20971410.18012093X-RAY DIFFRACTION99
2.5306-2.64580.22311420.17512100X-RAY DIFFRACTION100
2.6458-2.78530.25241410.17722096X-RAY DIFFRACTION100
2.7853-2.95970.19891430.18342107X-RAY DIFFRACTION99
2.9597-3.18820.19451430.18492121X-RAY DIFFRACTION99
3.1882-3.5090.2051430.1772119X-RAY DIFFRACTION100
3.509-4.01650.18451440.15722141X-RAY DIFFRACTION99
4.0165-5.05960.17171480.15422199X-RAY DIFFRACTION100
5.0596-48.78270.23081540.20482267X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9238-0.15680.0780.12510.24680.47270.13370.0887-0.2024-0.3301-0.12490.16440.16530.04680.01350.16550.0164-0.0080.15960.00510.099915.326692.7499154.9969
20.16390.2797-0.12790.4055-0.17780.5969-0.1065-0.0646-0.06760.12750.12720.20070.0601-0.09260.00020.14340.0082-0.00060.13890.01370.118610.1237102.714164.8905
30.5209-0.10070.33970.588-0.28430.3119-0.0588-0.00110.15360.12940.0238-0.21620.0050.0113-0.00140.14360.0041-0.0010.14040.01220.113416.8088109.6476163.1399
40.91590.3598-0.45791.141-0.15630.9115-0.05860.0595-0.15170.0674-0.0099-0.14540.0958-0.0061-0.14660.17320.01430.01610.1646-0.06170.235817.950168.0621138.0931
50.2161-0.05640.15850.0586-0.00720.283-0.04140.051-0.12690.10720.0310.3148-0.037-0.2107-0.00860.1335-0.01540.00680.2147-0.0470.20895.105674.2514140.7154
60.31870.1650.0110.12880.08430.12630.01810.04290.1060.1876-0.1559-0.1002-0.0196-0.0677-0.00030.15470.005-0.00520.1585-0.02830.148311.593180.0683148.4428
70.47830.1636-0.15790.2478-0.17470.5619-0.1726-0.0444-0.0980.0910.3015-0.37770.03280.13730.00590.1480.0123-0.00240.1719-0.01640.187321.583472.5201142.595
80.4857-0.04670.04760.33030.30630.4332-0.15860.1885-0.0992-0.21470.05390.0676-0.1516-0.0122-0.00970.175-0.0190.02280.1845-0.06060.224613.585775.0598133.9417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 46 through 99 )
2X-RAY DIFFRACTION2chain 'D' and (resid 100 through 178 )
3X-RAY DIFFRACTION3chain 'D' and (resid 179 through 256 )
4X-RAY DIFFRACTION4chain 'D' and (resid 257 through 304 )
5X-RAY DIFFRACTION5chain 'E' and (resid 13 through 43 )
6X-RAY DIFFRACTION6chain 'E' and (resid 44 through 67 )
7X-RAY DIFFRACTION7chain 'E' and (resid 68 through 95 )
8X-RAY DIFFRACTION8chain 'E' and (resid 96 through 122 )

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