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- PDB-4fhr: Crystal structure of the complex between the flagellar motor prot... -

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Basic information

Entry
Database: PDB / ID: 4fhr
TitleCrystal structure of the complex between the flagellar motor proteins FliG and FliM.
Components
  • Flagellar motor switch protein FliGFlagellar motor switch protein
  • Flagellar motor switch protein FliMFlagellar motor switch protein
KeywordsMOTOR PROTEIN / flagellar motor
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: 1.931 Å
AuthorsPaz, A. / Vartanian, A.S. / Fortgang, E.A. / Abramson, J. / Dahlquist, F.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of flagellar motor proteins in complex allows for insights into motor structure and switching.
Authors: Vartanian, A.S. / Paz, A. / Fortgang, E.A. / Abramson, J. / Dahlquist, F.W.
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Sep 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


Theoretical massNumber of molelcules
Total (without water)46,0952
Polymers46,0952
Non-polymers00
Water1,946108
1
A: Flagellar motor switch protein FliM


Theoretical massNumber of molelcules
Total (without water)21,4911
Polymers21,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)24,6051
Polymers24,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.960, 45.720, 98.840
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 21490.619 Da / Num. of mol.: 1 / Fragment: Middle domain, UNP residues 46-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: FliM / Plasmid: pJY5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Rosetta / References: UniProt: Q9WZE6
#2: Protein Flagellar motor switch protein FliG / Flagellar motor switch protein


Mass: 24604.529 Da / Num. of mol.: 1
Fragment: Middle and C-terminal domains. UNP residues 115-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: fliG / Plasmid: pJY5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Rosetta / References: UniProt: Q9WY63
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM calcium acetate, 0.1 M sodium cacodylate pH 6.0, and 25% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 41987 / Num. obs: 38741 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.93→2 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HP7

2hp7


Resolution: 1.931→48.537 Å / SU ML: 0.2 / σ(F): 0.1 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1968 5.08 %
Rwork0.2084 --
obs0.2102 38741 92.29 %
all-38740 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4488 Å20 Å2-0.3035 Å2
2--3.2599 Å2-0 Å2
3----2.8111 Å2
Refinement stepCycle: LAST / Resolution: 1.931→48.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 108 3246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083207
X-RAY DIFFRACTIONf_angle_d1.0594340
X-RAY DIFFRACTIONf_dihedral_angle_d15.6241239
X-RAY DIFFRACTIONf_chiral_restr0.07506
X-RAY DIFFRACTIONf_plane_restr0.006560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9311-1.97940.3104890.27241583X-RAY DIFFRACTION55
1.9794-2.03290.33641270.26542389X-RAY DIFFRACTION86
2.0329-2.09270.29691400.24582601X-RAY DIFFRACTION92
2.0927-2.16030.29931390.23812601X-RAY DIFFRACTION92
2.1603-2.23750.27881390.23472603X-RAY DIFFRACTION92
2.2375-2.32710.24741410.21742649X-RAY DIFFRACTION94
2.3271-2.4330.26161440.21222692X-RAY DIFFRACTION95
2.433-2.56120.23731470.2142750X-RAY DIFFRACTION97
2.5612-2.72170.26751470.22712756X-RAY DIFFRACTION97
2.7217-2.93180.26631480.22182789X-RAY DIFFRACTION98
2.9318-3.22680.23181520.2212836X-RAY DIFFRACTION99
3.2268-3.69360.25851520.20412844X-RAY DIFFRACTION100
3.6936-4.6530.19821530.17222859X-RAY DIFFRACTION99
4.653-48.55190.20381500.18552821X-RAY DIFFRACTION95

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