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- PDB-3a7m: Structure of FliT, the flagellar type III chaperone for FliD -

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Basic information

Entry
Database: PDB / ID: 3a7m
TitleStructure of FliT, the flagellar type III chaperone for FliD
ComponentsFlagellar protein fliT
KeywordsGENE REGULATION / CHAPERONE / Up-down helix bundle / Bacterial flagellum biogenesis / Cytoplasm / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum organization / protein folding / identical protein binding / cytosol
Similarity search - Function
Flagellar protein flit. / Flagellar protein FliT / Flagellar protein FliT / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar protein FliT
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsImada, K. / Minamino, T. / Kinoshita, M. / Namba, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural insight into the regulatory mechanisms of interactions of the flagellar type III chaperone FliT with its binding partners.
Authors: Imada, K. / Minamino, T. / Kinoshita, M. / Furukawa, Y. / Namba, K.
History
DepositionSep 29, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar protein fliT
B: Flagellar protein fliT


Theoretical massNumber of molelcules
Total (without water)27,8062
Polymers27,8062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-28 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.340, 121.340, 58.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsAUTHOR DEFINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Flagellar protein fliT


Mass: 13903.202 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SJW1103 / Gene: fliT, STM1962 / Plasmid: PET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P0A1N2
Has protein modificationY

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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: 4.49 Å3/Da / Density % sol: 72.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1M Potassium sodium tartrate, 0.1M CHES, 0.2M Li2SO4, pH9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 35 K / Ambient temp details: He gas cooling cryo system
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.2→42.2 Å / Num. all: 8390 / Num. obs: 8390 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 70.1 Å2 / Rsym value: 0.101 / Net I/σ(I): 11.1
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1219 / Rsym value: 0.402 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→42.19 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1423711.61 / 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
Rfree0.286 826 9.9 %RANDOM
Rwork0.252 ---
obs0.252 8376 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.7012 Å2 / ksol: 0.403934 e/Å3
Displacement parametersBiso mean: 52.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å216.45 Å20 Å2
2--0.83 Å20 Å2
3----1.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.2→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 0 0 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 132 9.6 %
Rwork0.317 1237 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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