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- PDB-3vjp: Orthorhombic Crystal Structure of Salmonella FlgA in closed form -

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Basic information

Entry
Database: PDB / ID: 3vjp
TitleOrthorhombic Crystal Structure of Salmonella FlgA in closed form
ComponentsFlagella basal body P-ring formation protein flgA
KeywordsCHAPERONE / BACTERIAL FLAGELLUM / SECRETION / DISULFIDE BOND
Function / homology
Function and homology information


bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / periplasmic space
Similarity search - Function
SH3 type barrels. - #760 / Flagella basal body P-ring formation protein FlgA, C-terminal / Flagellar protein FlgA / Chaperone for flagella basal body P-ring formation / SAF domain / SAF / SAF domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Flagella basal body P-ring formation protein FlgA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsMatsunami, H. / Samatey, F.A. / Namba, K.
CitationJournal: Sci Rep / Year: 2016
Title: Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica
Authors: Matsunami, H. / Yoon, Y.H. / Meshcheryakov, V.A. / Namba, K. / Samatey, F.A.
History
DepositionOct 27, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Nov 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagella basal body P-ring formation protein flgA
B: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)47,6872
Polymers47,6872
Non-polymers00
Water81145
1
A: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,8431
Polymers23,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,8431
Polymers23,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.168, 162.502, 103.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

21A-242-

HOH

31A-251-

HOH

41A-252-

HOH

51B-228-

HOH

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Components

#1: Protein Flagella basal body P-ring formation protein flgA / Flagellar flga protein


Mass: 23843.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SJW1103 / Gene: flgA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40131
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 12% PEG 6000, 0.1M CITRIC ACID, 1.0M LiCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97895 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 18, 2009
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.7→40.63 Å / Num. all: 12420 / Num. obs: 12420 / % possible obs: 98.69 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.85 Å / Mean I/σ(I) all: 1.61 / Num. measured all: 12094 / % possible all: 99.74

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9data scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→24.545 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.77 / σ(F): 1.36 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 602 4.85 %RANDOM
Rwork0.2438 11800 --
obs0.2453 12402 97.65 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.042 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 161.31 Å2 / Biso mean: 72.9635 Å2 / Biso min: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1-18.6857 Å20 Å2-0 Å2
2--2.463 Å20 Å2
3----21.1487 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 0 45 3035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043032
X-RAY DIFFRACTIONf_angle_d1.0444120
X-RAY DIFFRACTIONf_chiral_restr0.078484
X-RAY DIFFRACTIONf_plane_restr0.006550
X-RAY DIFFRACTIONf_dihedral_angle_d15.7431124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.97130.33551560.305829503106100
2.9713-3.40030.36211570.26362933309099
3.4003-4.28040.24631500.23262953310398
4.2804-24.5460.2511390.22882964310394

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