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- PDB-6ai1: Structure of the 328-692 fragment of FlhA (D456V) -

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Basic information

Entry
Database: PDB / ID: 6ai1
TitleStructure of the 328-692 fragment of FlhA (D456V)
ComponentsFlagellar biosynthesis protein FlhA
KeywordsPROTEIN TRANSPORT / flagellar type III secretion
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsOgawa, Y. / Kinoshita, M. / Minamino, T. / Imada, K.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP15H02386 Japan
Japan Society for the Promotion of ScienceJP26293097 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP23115008 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP24117004 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP25121718 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP15H01640 Japan
CitationJournal: Structure / Year: 2019
Title: Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus.
Authors: Inoue, Y. / Ogawa, Y. / Kinoshita, M. / Terahara, N. / Shimada, M. / Kodera, N. / Ando, T. / Namba, K. / Kitao, A. / Imada, K. / Minamino, T.
History
DepositionAug 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 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: Flagellar biosynthesis protein FlhA
B: Flagellar biosynthesis protein FlhA


Theoretical massNumber of molelcules
Total (without water)81,3112
Polymers81,3112
Non-polymers00
Water0
1
A: Flagellar biosynthesis protein FlhA


Theoretical massNumber of molelcules
Total (without water)40,6561
Polymers40,6561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar biosynthesis protein FlhA


Theoretical massNumber of molelcules
Total (without water)40,6561
Polymers40,6561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.790, 216.790, 64.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Flagellar biosynthesis protein FlhA


Mass: 40655.688 Da / Num. of mol.: 2 / Fragment: cytoplasmic fragment, residues 328-692 / Mutation: D456V
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: flhA, STM1913 / Plasmid: pGEX6p1
Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain (production host): SJW1368 / References: UniProt: P40729

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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: 4.69 Å3/Da / Density % sol: 73.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG-400, 0.1M HEPES pH 7.5, 0.25M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→68.6 Å / Num. obs: 19380 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.6
Reflection shellResolution: 3.5→3.83 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4609 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A5I

3a5i


Resolution: 3.5→54.198 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.37
RfactorNum. reflection% reflection
Rfree0.2412 1969 10.17 %
Rwork0.1891 --
obs0.1944 19369 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.04 Å2 / Biso mean: 94.8251 Å2 / Biso min: 39.19 Å2
Refinement stepCycle: final / Resolution: 3.5→54.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 0 0 5344
Num. residues----690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115436
X-RAY DIFFRACTIONf_angle_d1.2397386
X-RAY DIFFRACTIONf_chiral_restr0.06868
X-RAY DIFFRACTIONf_plane_restr0.008968
X-RAY DIFFRACTIONf_dihedral_angle_d19.7752050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5002-3.58770.36541490.292312211370100
3.5877-3.68470.32671620.250411981360100
3.6847-3.79310.29711420.235512591401100
3.7931-3.91550.27171700.229312011371100
3.9155-4.05540.27551180.212412591377100
4.0554-4.21770.22871360.203212441380100
4.2177-4.40960.27391500.19411971347100
4.4096-4.64190.2421310.187812611392100
4.6419-4.93260.21931460.170312291375100
4.9326-5.31310.27081180.182312601378100
5.3131-5.84730.22581570.194712471404100
5.8473-6.6920.22861320.191112481380100
6.692-8.42610.19441100.1691288139899
8.4261-54.2040.18781480.14281288143698

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