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- PDB-3soh: Architecture of the Flagellar Rotor -

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Basic information

Entry
Database: PDB / ID: 3soh
TitleArchitecture of the Flagellar Rotor
Components
  • Flagellar motor switch protein FliGFlagellar motor switch protein
  • Flagellar motor switch protein FliMFlagellar motor switch protein
KeywordsMOTOR PROTEIN / protein-protein complex / alpha/beta
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / protein heterodimerization activity / protein homodimerization activity / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliG, alpha-alpha superhelical domain / CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliG / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain ...Flagellar motor switch protein FliG, alpha-alpha superhelical domain / CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliG / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / Flagellar motor switch protein FliM / FliG middle domain / FliG N-terminal domain / 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 / Annexin V; domain 1 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Flagellar motor switch protein FliM
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKoushik, P. / Gonzalez-Bonet, G. / Bilwes, A.M. / Crane, B.R. / Blair, D.
CitationJournal: Embo J. / Year: 2011
Title: Architecture of the flagellar rotor.
Authors: Paul, K. / Gonzalez-Bonet, G. / Bilwes, A.M. / Crane, B.R. / Blair, D.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Sep 13, 2023Group: 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 / 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: Flagellar motor switch protein FliM
B: Flagellar motor switch protein FliG
C: Flagellar motor switch protein FliM
D: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)61,4974
Polymers61,4974
Non-polymers00
Water181
1
A: Flagellar motor switch protein FliM
B: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)30,7482
Polymers30,7482
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Flagellar motor switch protein FliM
D: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)30,7482
Polymers30,7482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.390, 91.390, 226.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 21797.041 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 46-233)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0679 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZE6
#2: Protein Flagellar motor switch protein FliG / Flagellar motor switch protein


Mass: 8951.303 Da / Num. of mol.: 2 / Fragment: middle domain (UNP residues 117-193)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: fliG, TM_0220 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WY63
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.49 Å3/Da / Density % sol: 72.59 %
Crystal growMethod: evaporation / pH: 6.5
Details: 0.1 M MES, pH 6.5, 10% dioxane, 1.6 M ammonium sulfate, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→26.21 Å / Num. all: 13308 / Num. obs: 13308 / % possible obs: 91.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 78.6 Å2 / Rsym value: 0.0919 / Net I/σ(I): 20.5
Reflection shellResolution: 3.5→3.63 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.358 / % possible all: 84.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2HP7 AND 1LKV

2hp7

1lkv


Resolution: 3.5→26.21 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 57158.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1275 10.1 %RANDOM
Rwork0.253 ---
obs0.253 12574 87.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.3469 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 128.4 Å2
Baniso -1Baniso -2Baniso -3
1-33.21 Å20 Å20 Å2
2--33.21 Å20 Å2
3----66.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.95 Å0.89 Å
Refinement stepCycle: LAST / Resolution: 3.5→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 0 1 4285
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it15.761.5
X-RAY DIFFRACTIONc_mcangle_it23.982
X-RAY DIFFRACTIONc_scbond_it23.992
X-RAY DIFFRACTIONc_scangle_it33.172.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.445 189 10.3 %
Rwork0.406 1648 -
obs--78.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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