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- PDB-1io1: CRYSTAL STRUCTURE OF F41 FRAGMENT OF FLAGELLIN -

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Basic information

Entry
Database: PDB / ID: 1io1
TitleCRYSTAL STRUCTURE OF F41 FRAGMENT OF FLAGELLIN
ComponentsPHASE 1 FLAGELLIN
KeywordsSTRUCTURAL PROTEIN / beta-folium / flagellin
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / bacterial-type flagellum / receptor ligand activity / structural molecule activity / extracellular space
Similarity search - Function
f41 fragment of flagellin, middle domain / f41 fragment of flagellin, middle domain / f41 fragment of flagellin, C-terminal domain / f41 fragment of flagellin, C-terminal domain / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain ...f41 fragment of flagellin, middle domain / f41 fragment of flagellin, middle domain / f41 fragment of flagellin, C-terminal domain / f41 fragment of flagellin, C-terminal domain / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Beta Complex / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSamatey, F.A. / Imada, K. / Nagashima, S. / Vondervisz, F. / Kumasaka, T. / Yamamoto, M. / Namba, K.
CitationJournal: Nature / Year: 2001
Title: Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling.
Authors: F A Samatey / K Imada / S Nagashima / F Vonderviszt / T Kumasaka / M Yamamoto / K Namba /
Abstract: The bacterial flagellar filament is a helical propeller constructed from 11 protofilaments of a single protein, flagellin. The filament switches between left- and right-handed supercoiled forms when ...The bacterial flagellar filament is a helical propeller constructed from 11 protofilaments of a single protein, flagellin. The filament switches between left- and right-handed supercoiled forms when bacteria switch their swimming mode between running and tumbling. Supercoiling is produced by two different packing interactions of flagellin called L and R. In switching from L to R, the intersubunit distance ( approximately 52 A) along the protofilament decreases by 0.8 A. Changes in the number of L and R protofilaments govern supercoiling of the filament. Here we report the 2.0 A resolution crystal structure of a Salmonella flagellin fragment of relative molecular mass 41,300. The crystal contains pairs of antiparallel straight protofilaments with the R-type repeat. By simulated extension of the protofilament model, we have identified possible switch regions responsible for the bi-stable mechanical switch that generates the 0.8 A difference in repeat distance.
History
DepositionDec 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHASE 1 FLAGELLIN


Theoretical massNumber of molelcules
Total (without water)41,3521
Polymers41,3521
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.750, 36.440, 118.350
Angle α, β, γ (deg.)90.00, 91.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHASE 1 FLAGELLIN


Mass: 41351.969 Da / Num. of mol.: 1 / Fragment: F41 L-TYPE (RESIDUES 54-451) / Mutation: G426A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SJW 1660 / Production host: Escherichia coli (E. coli) / References: UniProt: P06179
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 6000, NaCl, Glycerol, Iso-Propanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
26 %PEG60001reservoir
312 %glycerol1reservoir
43-6 %isopropanol1reservoir
550-75 mM1reservoirNaCl
620 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 1999
RadiationMonochromator: Diamond 111 + Germanium 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→31.6 Å / Num. all: 121314 / Num. obs: 121314 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.47 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.272 / % possible all: 97
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 2467 random
Rwork0.234 --
all-34961 -
obs-29866 -
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2880 0 0 354 3234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.523
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.09 Å / Rfactor Rfree: 0.308 / Rfactor Rwork: 0.309 / Num. reflection Rwork: 3615

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