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- PDB-3tee: Crystal Structure of Salmonella FlgA in open form -

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Open data


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Basic information

Entry
Database: PDB / ID: 3tee
TitleCrystal Structure of Salmonella FlgA in open form
ComponentsFlagella basal body P-ring formation protein flgA
KeywordsCHAPERONE / Flagellar P-ring formation / Flagellar FlgI protein / Periplasmic protein
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 / MAD / Resolution: 1.95 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
DepositionAug 12, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Nov 20, 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_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: Flagella basal body P-ring formation protein flgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1527
Polymers23,6561
Non-polymers4966
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.520, 131.770, 49.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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.: 1
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 18% PEG 2000, 0.8M lithium chloride, 0.05M citric acid, 18% glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.983
SYNCHROTRONSPring-8 BL41XU21.07153, 1.07188, 1.09074
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 27, 2007
ADSC QUANTUM 3152CCDJun 27, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE-CRYSTAL MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2DOUBLE-CRYSTAL MONOCHROMATORMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9831
21.071531
31.071881
41.090741
ReflectionResolution: 1.95→34.58 Å / Num. all: 25669 / Num. obs: 25669 / % possible obs: 98.69 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 38.42 Å2 / Rsym value: 0.069 / Net I/σ(I): 12.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3686 / Rsym value: 0.372 / % possible all: 98.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→31.2 Å / Cor.coef. Fo:Fc: 0.9446 / Cor.coef. Fo:Fc free: 0.9245 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1302 5.07 %RANDOM
Rwork0.2003 ---
obs0.2012 25665 --
all-25665 --
Displacement parametersBiso max: 133.94 Å2 / Biso mean: 50.9026 Å2 / Biso min: 23.46 Å2
Baniso -1Baniso -2Baniso -3
1--9.2112 Å20 Å20 Å2
2--5.9051 Å20 Å2
3---3.3062 Å2
Refine analyzeLuzzati coordinate error obs: 0.255 Å
Refinement stepCycle: LAST / Resolution: 1.95→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 31 166 1752
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d564SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes227HARMONIC5
X-RAY DIFFRACTIONt_it1599HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion211SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1908SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1599HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2162HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion16.75
LS refinement shellResolution: 1.95→2.03 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2184 139 4.85 %
Rwork0.2091 2725 -
all0.2096 2864 -
obs-2864 -
Refinement TLS params.Method: refined / Origin x: 14.6614 Å / Origin y: 36.0775 Å / Origin z: 15.3626 Å
111213212223313233
T-0.2565 Å20.0377 Å2-0.0783 Å2--0.2856 Å2-0.0599 Å2---0.2787 Å2
L0.4791 °2-0.3443 °20.0878 °2-0.5702 °2-0.2655 °2--0.1765 °2
S0.041 Å °0.0282 Å °-0.1577 Å °-0.0199 Å °0.1098 Å °-0.0633 Å °0.1035 Å °0.0295 Å °-0.1508 Å °
Refinement TLS groupSelection details: { A|* }

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