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- PDB-3a5i: Structure of the cytoplasmic domain of FlhA -

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Basic information

Entry
Database: PDB / ID: 3a5i
TitleStructure of the cytoplasmic domain of FlhA
ComponentsFlagellar biosynthesis protein flhA
KeywordsPROTEIN TRANSPORT / four domains / thioredoxin-like fold / Bacterial flagellum biogenesis / Bacterial flagellum protein export / Cell inner membrane / Cell membrane / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


bacterial-type flagellum assembly / protein secretion / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin ...Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar biosynthesis protein FlhA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsImada, K. / Saijo-Hamano, Y. / Shimada, M. / Namba, K.
Citation
Journal: Mol.Microbiol. / Year: 2010
Title: Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export
Authors: Saijo-Hamano, Y. / Imada, K. / Minamino, T. / Kihara, M. / Shimada, M. / Kitao, A. / Namba, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and preliminary X-ray analysis of the C-terminal cytoplasmic domain of FlhA, a membrane-protein subunit of the bacterial flagellar type III protein-export apparatus
Authors: Saijo-Hamano, Y. / Imada, K. / Minamino, T. / Kihara, M. / Macnab, R.M. / Namba, K.
History
DepositionAug 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Flagellar biosynthesis protein flhA
B: Flagellar biosynthesis protein flhA


Theoretical massNumber of molelcules
Total (without water)86,5172
Polymers86,5172
Non-polymers00
Water00
1
A: Flagellar biosynthesis protein flhA


Theoretical massNumber of molelcules
Total (without water)43,2581
Polymers43,2581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagellar biosynthesis protein flhA


Theoretical massNumber of molelcules
Total (without water)43,2581
Polymers43,2581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)216.323, 216.323, 65.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Flagellar biosynthesis protein flhA


Mass: 43258.348 Da / Num. of mol.: 2 / Fragment: FlhAc, UNP residues 328-692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SJW1103 / Gene: flhA, STM1913 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P40729

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.472.04
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10-15% PEG300, 4-6% PEG8000, 0.1M Tris-HCl, 0.5mM EDTA, 10-15% glycerol, pH8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.9794, 0.9796, 0.9843
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 16, 2004
MARRESEARCH2CCDJun 16, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Double-crystal monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
30.97961
40.98431
ReflectionResolution: 2.8→40.8 Å / Num. all: 37317 / Num. obs: 37317 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 85.2 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3 / Num. unique all: 5343 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→40.8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2106476.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1863 5 %RANDOM
Rwork0.257 ---
obs0.257 37317 99.5 %-
all-37317 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0094 Å2 / ksol: 0.29557 e/Å3
Displacement parametersBiso mean: 75.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.13 Å20 Å20 Å2
2---3.13 Å20 Å2
3---6.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.8→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5336 0 0 0 5336
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.423 291 4.8 %
Rwork0.4 5807 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.param

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