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- PDB-2hp7: Structure of FliM provides insight into assembly of the switch co... -

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Basic information

Entry
Database: PDB / ID: 2hp7
TitleStructure of FliM provides insight into assembly of the switch complex in the bacterial flagella motor
ComponentsFlagellar motor switch protein FliMFlagellar motor switch protein
KeywordsSIGNALING PROTEIN / bacterial chemotaxis / flagellar switch complex
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / plasma membrane
Similarity search - Function
CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / CheC-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliM
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCrane, B.R. / Park, S. / Lowder, B. / Bilwes, A.M. / Blair, D.F.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of FliM provides insight into assembly of the switch complex in the bacterial flagella motor.
Authors: Park, S. / Lowder, B. / Bilwes, A.M. / Blair, D.F. / Crane, B.R.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300Author states that biological unit for the protein is not yet known

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar motor switch protein FliM


Theoretical massNumber of molelcules
Total (without water)21,0441
Polymers21,0441
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.367, 53.367, 130.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsbiological assembly not known. One molecule per AU

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Components

#1: Protein Flagellar motor switch protein FliM / Flagellar motor switch protein


Mass: 21044.137 Da / Num. of mol.: 1 / Fragment: CheC-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZE6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.244.05
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop8.530-40% PEG 4K, 0.1M TrisHCL pH 8.5, 0.2 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop7.50.8 M Na K tartrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F210.9795
SYNCHROTRONNSLS X2521.0062, 1.00936, 0.9686
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 20, 2005
ADSC QUANTUM 3152CCDJan 29, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.00621
31.009361
40.96861
ReflectionResolution: 2→30 Å / Num. obs: 12473 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 31
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 11 / % possible all: 96.3

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.249 1283 10 %
Rwork0.224 --
obs0.224 12473 97.7 %
all-12473 -
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--0.061 Å20 Å20 Å2
2---0.061 Å20 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 0 190 1645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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