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- PDB-3vki: Monoclinic Crystal Structure of Salmonella FlgA in closed form -

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Basic information

Entry
Database: PDB / ID: 3vki
TitleMonoclinic 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 / 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 domain / SAF / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionNov 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references

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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
C: Flagella basal body P-ring formation protein flgA
D: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)94,6234
Polymers94,6234
Non-polymers00
Water3,351186
1
A: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,6561
Polymers23,6561
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)23,6561
Polymers23,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,6561
Polymers23,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,6561
Polymers23,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.926, 103.317, 85.501
Angle α, β, γ (deg.)90.000, 107.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23655.721 Da / Num. of mol.: 4
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.: 186 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 12% PEG 6000, 0.05M CITRIC ACID PH 4.2, 1.0M LICl, 14% 2-METHYL-2,4-PENTANEDIOL, 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: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 19, 2011
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40.8 Å / Num. obs: 39534 / % possible obs: 99.3 %
Reflection shellResolution: 2.3→2.42 Å / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.3.16data scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7739 / SU ML: 0.86 / σ(F): 0 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 1983 5.02 %RANDOM
Rwork0.2513 ---
obs0.2529 39492 99.26 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.642 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 143.44 Å2 / Biso mean: 60.0246 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1-11.3415 Å2-0 Å2-0.8884 Å2
2---11.4207 Å2-0 Å2
3---0.0792 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 0 186 6166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046064
X-RAY DIFFRACTIONf_angle_d0.9698240
X-RAY DIFFRACTIONf_chiral_restr0.075968
X-RAY DIFFRACTIONf_plane_restr0.0031100
X-RAY DIFFRACTIONf_dihedral_angle_d16.6782248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.33271510.30242491264293
2.3575-2.42120.37991470.30212646279399
2.4212-2.49240.29221290.305327002829100
2.4924-2.57270.39161320.288427262858100
2.5727-2.66460.34751390.288126542793100
2.6646-2.77110.31221480.270726912839100
2.7711-2.89710.31911320.253926942826100
2.8971-3.04960.28321660.262527002866100
3.0496-3.24030.28281350.258126852820100
3.2403-3.48980.26631480.251326722820100
3.4898-3.83990.29521460.241727262872100
3.8399-4.39290.24971430.222427032846100
4.3929-5.52470.23061290.223927302859100
5.5247-24.98560.26091380.25122691282997

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