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- PDB-3ajw: Structure of FliJ, a soluble component of flagellar type III expo... -

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Basic information

Entry
Database: PDB / ID: 3ajw
TitleStructure of FliJ, a soluble component of flagellar type III export apparatus
ComponentsFlagellar fliJ protein
KeywordsPROTEIN TRANSPORT / Flagellum / type III secretion / Coiled-coil
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / protein transport / plasma membrane
Similarity search - Function
Flagellar export FliJ / Flagellar FliJ, proteobacteria / Flagellar FliJ protein / Helix Hairpins - #1700 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Flagellar FliJ protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsImada, K. / Ibuki, T. / Minamino, T. / Namba, K.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Common architecture of the flagellar type III protein export apparatus and F- and V-type ATPases
Authors: Ibuki, T. / Imada, K. / Minamino, T. / Kato, T. / Miyata, T. / Namba, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and preliminary X-ray analysis of FliJ, a cytoplasmic component of the flagellar type III protein-export apparatus from Salmonella sp
Authors: Ibuki, T. / Shimada, M. / Minamino, T. / Namba, K. / Imada, K.
History
DepositionJun 23, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar fliJ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8302
Polymers17,6291
Non-polymers2011
Water2,846158
1
A: Flagellar fliJ protein
hetero molecules

A: Flagellar fliJ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6594
Polymers35,2582
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Buried area3120 Å2
ΔGint-17 kcal/mol
Surface area17910 Å2
MethodPISA
2
A: Flagellar fliJ protein
hetero molecules

A: Flagellar fliJ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6594
Polymers35,2582
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Buried area1750 Å2
ΔGint-8 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.925, 52.925, 192.597
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN.

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Components

#1: Protein Flagellar fliJ protein


Mass: 17628.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SJW1103 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P0A1K1
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 27% PEG 300, 0.1M Phospho-Citrate, 0.35M NaCl, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 35 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.0082 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2007
RadiationMonochromator: Double-crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0082 Å / Relative weight: 1
ReflectionResolution: 2.1→38.52 Å / Num. all: 10032 / Num. obs: 10032 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.087 / Net I/σ(I): 25
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 7 / Num. unique all: 1426 / Rsym value: 0.347 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→37.3 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1867106.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 480 4.8 %RANDOM
Rwork0.232 ---
obs0.232 10032 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.2942 Å2 / ksol: 0.471619 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.18 Å22.22 Å20 Å2
2--6.18 Å20 Å2
3----12.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.04 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 1 158 1265
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.6
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it2.852
X-RAY DIFFRACTIONc_scangle_it4.442.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 76 4.7 %
Rwork0.215 1531 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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