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- PDB-9uwz: Crystal structure of the type III secretion chaperone VecA from V... -

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Basic information

Entry
Database: PDB / ID: 9uwz
TitleCrystal structure of the type III secretion chaperone VecA from Vibrio parahaemolyticus
ComponentsCesT family type III secretion system chaperone
KeywordsCHAPERONE / Vibrio parahaemolyticus / Type 3 secretion system
Function / homologyTir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / protein secretion by the type III secretion system / PHOSPHATE ION / HEXATANTALUM DODECABROMIDE / CesT family type III secretion system chaperone
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsIimori, M. / Oki, H. / Akeda, Y. / Ishii, E. / Kodama, T. / Ueda, T. / Nakamura, S. / Matsuda, S. / Kawahara, K. / Iida, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP24KJ1623 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural basis of effector recognition by the T3SS chaperone VecA from Vibrio parahaemolyticus.
Authors: Iimori, M. / Oki, H. / Akeda, Y. / Ishii, E. / Kodama, T. / Ueda, T. / Nakamura, S. / Matsuda, S. / Kawahara, K. / Iida, T.
History
DepositionMay 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CesT family type III secretion system chaperone
B: CesT family type III secretion system chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2474
Polymers35,1082
Non-polymers2,1402
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-13 kcal/mol
Surface area14780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.754, 73.754, 109.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein CesT family type III secretion system chaperone


Mass: 17553.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP1682 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87P37
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Br12Ta6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl (pH 8.8), 1.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.2538 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2538 Å / Relative weight: 1
ReflectionResolution: 2.2→47.12 Å / Num. obs: 16059 / % possible obs: 100 % / Redundancy: 23.8 % / Biso Wilson estimate: 55.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.025 / Rrim(I) all: 0.122 / Χ2: 1.05 / Net I/σ(I): 20.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 24.6 % / Rmerge(I) obs: 1.612 / Num. unique obs: 1354 / CC1/2: 0.794 / Rpim(I) all: 0.329 / Rrim(I) all: 1.646 / Χ2: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.2→32.81 Å / SU ML: 0.2973 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 29.4287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2949 1612 10.08 %
Rwork0.2393 14387 -
obs0.2448 15999 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.97 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 23 18 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872170
X-RAY DIFFRACTIONf_angle_d1.06973074
X-RAY DIFFRACTIONf_chiral_restr0.053332
X-RAY DIFFRACTIONf_plane_restr0.0107380
X-RAY DIFFRACTIONf_dihedral_angle_d18.8638794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.34581250.30371167X-RAY DIFFRACTION100
2.26-2.340.32671440.28271150X-RAY DIFFRACTION99.85
2.34-2.420.34021340.29841170X-RAY DIFFRACTION100
2.42-2.520.3461270.27081182X-RAY DIFFRACTION100
2.52-2.630.32691360.27671190X-RAY DIFFRACTION100
2.63-2.770.31471260.2561177X-RAY DIFFRACTION100
2.77-2.950.25621410.26711183X-RAY DIFFRACTION100
2.95-3.170.29351330.26921187X-RAY DIFFRACTION100
3.17-3.490.30241390.24261202X-RAY DIFFRACTION100
3.49-3.990.26631170.22341232X-RAY DIFFRACTION100
4-5.030.29111290.20511240X-RAY DIFFRACTION99.93
5.03-32.810.29481610.23771307X-RAY DIFFRACTION99.93

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