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- PDB-5tdy: Structure of cofolded FliFc:FliGn complex from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 5tdy
TitleStructure of cofolded FliFc:FliGn complex from Thermotoga maritima
Components
  • Flagellar M-ring protein
  • Flagellar motor switch protein FliG
KeywordsMOTOR PROTEIN / flagellar motor / switch complex
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / membrane => GO:0016020 / protein heterodimerization activity / protein homodimerization activity / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliG / 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 / FliG middle domain / FliG N-terminal domain / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal ...Flagellar motor switch protein FliG / 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 / FliG middle domain / FliG N-terminal domain / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Flagellar M-ring protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.105 Å
AuthorsLynch, M.J. / Levenson, R. / Kim, E.A. / Sircar, R. / Blair, D.F. / Dahlquist, F.W. / Crane, B.R.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008500 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM59544 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
CitationJournal: Structure / Year: 2017
Title: Co-Folding of a FliF-FliG Split Domain Forms the Basis of the MS:C Ring Interface within the Bacterial Flagellar Motor.
Authors: Lynch, M.J. / Levenson, R. / Kim, E.A. / Sircar, R. / Blair, D.F. / Dahlquist, F.W. / Crane, B.R.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 29, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar M-ring protein
B: Flagellar motor switch protein FliG
C: Flagellar M-ring protein
D: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)32,9074
Polymers32,9074
Non-polymers00
Water3,117173
1
A: Flagellar M-ring protein
B: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)16,4532
Polymers16,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-27 kcal/mol
Surface area9350 Å2
MethodPISA
2
C: Flagellar M-ring protein
D: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)16,4532
Polymers16,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-26 kcal/mol
Surface area8810 Å2
MethodPISA
3
A: Flagellar M-ring protein
B: Flagellar motor switch protein FliG

C: Flagellar M-ring protein
D: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)32,9074
Polymers32,9074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area8450 Å2
ΔGint-77 kcal/mol
Surface area15100 Å2
MethodPISA
4
A: Flagellar M-ring protein
B: Flagellar motor switch protein FliG

C: Flagellar M-ring protein
D: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)32,9074
Polymers32,9074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area6940 Å2
ΔGint-65 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.180, 59.327, 51.722
Angle α, β, γ (deg.)90.00, 115.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Flagellar M-ring protein


Mass: 5296.836 Da / Num. of mol.: 2 / Fragment: FliF C-terminal tail
Source method: isolated from a genetically manipulated source
Details: contains C-terminal linker sequence -LENLYF- / Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0221, Tmari_0219 / Plasmid: pJY5 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9WY64
#2: Protein Flagellar motor switch protein FliG


Mass: 11156.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: fliG, TM_0220 / Cell line (production host): B834 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9WY63
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.07 Å3/Da / Density % sol: 40.52 % / Description: cluster of plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Wild Type: 100 mM HEPES pH 7.5, 25% (w/v) PEG3000, 200 mM sodium chloride Selenomethionine: 100 mm imidazole pH 7.2, 30% (w/v) PEG8000, 130 mM sodium chloride
PH range: 7.2 - 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.977
SYNCHROTRONAPS 24-ID-E20.97921
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJun 20, 2014
ADSC QUANTUM 3152CCDOct 28, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9771
20.979211
Reflection

Entry-ID: 5TDY

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.1-501562199.53.10.082113.4
2.6-501582599.260.122214.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.105→46.647 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1556 9.96 %Random selection
Rwork0.1692 ---
obs0.174 15617 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.3 Å2
Refinement stepCycle: LAST / Resolution: 2.105→46.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 0 173 2263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072116
X-RAY DIFFRACTIONf_angle_d0.882833
X-RAY DIFFRACTIONf_dihedral_angle_d23.5591333
X-RAY DIFFRACTIONf_chiral_restr0.051321
X-RAY DIFFRACTIONf_plane_restr0.006363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1052-2.17310.2421410.17471280X-RAY DIFFRACTION99
2.1731-2.25080.22951410.17521288X-RAY DIFFRACTION100
2.2508-2.34090.23471420.16731270X-RAY DIFFRACTION100
2.3409-2.44740.23051390.1771271X-RAY DIFFRACTION100
2.4474-2.57640.20321430.16751281X-RAY DIFFRACTION100
2.5764-2.73780.24511440.1761270X-RAY DIFFRACTION100
2.7378-2.94920.21161410.16741265X-RAY DIFFRACTION100
2.9492-3.24590.2291320.16671294X-RAY DIFFRACTION100
3.2459-3.71550.21221430.15231283X-RAY DIFFRACTION99
3.7155-4.68040.181440.15741266X-RAY DIFFRACTION99
4.6804-46.65870.22631460.19111293X-RAY DIFFRACTION98

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