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- PDB-5b0o: Structure of the FliH-FliI complex -

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Basic information

Entry
Database: PDB / ID: 5b0o
TitleStructure of the FliH-FliI complex
Components
  • Flagellar assembly protein FliH
  • Flagellum-specific ATP synthase
KeywordsHYDROLASE/MOTOR PROTEIN / Bacterial flagellum / type III secretion / ATPase / peripheral stalk / HYDROLASE-MOTOR PROTEIN complex
Function / homology
Function and homology information


bacterial-type flagellum organization / type III protein secretion system complex / bacterial-type flagellum / protein secretion by the type III secretion system / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism ...bacterial-type flagellum organization / type III protein secretion system complex / bacterial-type flagellum / protein secretion by the type III secretion system / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / protein transport / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Flagellar assembly protein FliH / Flagellar assembly protein FliH/Type III secretion system HrpE / Flagellar assembly protein FliH / Flagellar export ATPase FliI, clade 1 / ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain ...Flagellar assembly protein FliH / Flagellar assembly protein FliH/Type III secretion system HrpE / Flagellar assembly protein FliH / Flagellar export ATPase FliI, clade 1 / ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Flagellar assembly protein FliH / Flagellum-specific ATP synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsImada, K. / Uchida, Y. / Kinoshita, M. / Namba, K. / Minamino, T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Insight into the flagella type III export revealed by the complex structure of the type III ATPase and its regulator
Authors: Imada, K. / Minamino, T. / Uchida, Y. / Kinoshita, M. / Namba, K.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: Crystallization and preliminary X-ray analysis of the FliH-FliI complex responsible for bacterial flagellar type III protein export.
Authors: Uchida, Y. / Minamino, T. / Namba, K. / Imada, K.
History
DepositionNov 2, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellum-specific ATP synthase
B: Flagellum-specific ATP synthase
C: Flagellum-specific ATP synthase
D: Flagellum-specific ATP synthase
E: Flagellar assembly protein FliH
F: Flagellar assembly protein FliH
G: Flagellar assembly protein FliH
H: Flagellar assembly protein FliH
I: Flagellar assembly protein FliH
J: Flagellar assembly protein FliH
K: Flagellar assembly protein FliH
L: Flagellar assembly protein FliH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,67116
Polymers319,96212
Non-polymers1,7094
Water0
1
A: Flagellum-specific ATP synthase
E: Flagellar assembly protein FliH
I: Flagellar assembly protein FliH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4184
Polymers79,9903
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellum-specific ATP synthase
F: Flagellar assembly protein FliH
J: Flagellar assembly protein FliH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4184
Polymers79,9903
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Flagellum-specific ATP synthase
G: Flagellar assembly protein FliH
K: Flagellar assembly protein FliH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4184
Polymers79,9903
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Flagellum-specific ATP synthase
H: Flagellar assembly protein FliH
L: Flagellar assembly protein FliH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4184
Polymers79,9903
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.662, 147.305, 164.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Flagellum-specific ATP synthase


Mass: 49319.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliI, fla AIII, flaC, STM1972 / Plasmid: pET15b / Production host: Escherichia coli / Strain (production host): BL21(DE3)
References: UniProt: P26465, H+-transporting two-sector ATPase
#2: Protein
Flagellar assembly protein FliH


Mass: 15335.442 Da / Num. of mol.: 8 / Fragment: UNP residues 99-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliH, fla AII.3, fla BIII, STM1971 / Production host: Escherichia coli (E. coli) / References: UniProt: P15934
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 5%(w/v) PEG400, 0.1M HEPES pH7.2 and 100mM Magnesium acetate

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Data collection

DiffractionMean temperature: 40 K / Ambient temp details: helium gas flow
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→60 Å / Num. obs: 65054 / % possible obs: 99.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
MOSFLMdata processing
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DPY

2dpy


Resolution: 3→51.315 Å / SU ML: 0.96 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 3292 5.07 %Random selection
Rwork0.2177 ---
obs0.2203 64990 99.18 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.271 Å2 / ksol: 0.267 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2768 Å20 Å2-0 Å2
2--9.0396 Å20 Å2
3----3.7628 Å2
Refinement stepCycle: LAST / Resolution: 3→51.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21874 0 108 0 21982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522369
X-RAY DIFFRACTIONf_angle_d0.99830354
X-RAY DIFFRACTIONf_dihedral_angle_d15.9618410
X-RAY DIFFRACTIONf_chiral_restr0.0663476
X-RAY DIFFRACTIONf_plane_restr0.0053990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04290.3881250.29492562X-RAY DIFFRACTION99
3.0429-3.08830.33771220.26762531X-RAY DIFFRACTION100
3.0883-3.13660.30031460.26112562X-RAY DIFFRACTION100
3.1366-3.1880.32291420.24462553X-RAY DIFFRACTION100
3.188-3.24290.3271300.25272569X-RAY DIFFRACTION100
3.2429-3.30190.3231490.24342538X-RAY DIFFRACTION100
3.3019-3.36540.3291430.24942575X-RAY DIFFRACTION100
3.3654-3.43410.32951340.2492571X-RAY DIFFRACTION100
3.4341-3.50870.30721410.25232532X-RAY DIFFRACTION100
3.5087-3.59030.34841160.27642608X-RAY DIFFRACTION100
3.5903-3.68010.41791360.372564X-RAY DIFFRACTION100
3.6801-3.77960.33461180.27882576X-RAY DIFFRACTION100
3.7796-3.89070.27251460.21062549X-RAY DIFFRACTION100
3.8907-4.01630.28521260.21362600X-RAY DIFFRACTION100
4.0163-4.15980.25771380.19092581X-RAY DIFFRACTION100
4.1598-4.32620.21791360.18092610X-RAY DIFFRACTION100
4.3262-4.5230.24861370.16852554X-RAY DIFFRACTION100
4.523-4.76130.24981360.16622591X-RAY DIFFRACTION100
4.7613-5.05940.19631570.16982577X-RAY DIFFRACTION100
5.0594-5.44960.21671370.19022588X-RAY DIFFRACTION99
5.4496-5.99730.23891410.20492577X-RAY DIFFRACTION99
5.9973-6.86340.2991500.22762595X-RAY DIFFRACTION99
6.8634-8.64040.23421480.18422612X-RAY DIFFRACTION98
8.6404-51.32270.20491380.18232523X-RAY DIFFRACTION91

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