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- PDB-8u2f: Vibrio parahaemolyticus ToxS periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 8u2f
TitleVibrio parahaemolyticus ToxS periplasmic domain
ComponentsTransmembrane regulatory protein ToxS
KeywordsMEMBRANE PROTEIN / transmembrane regulator / virulence / stress response / transcriptional regulation
Function / homologyTrans-membrane regulatory protein ToxS / Trans-membrane regulatory protein ToxS / plasma membrane / Transmembrane regulatory protein ToxS
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, M. / Kull, F.J. / Midgett, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Vibrio parahaemolyticus ToxS periplasmic domain
Authors: Kim, M. / Kull, F.J. / Midgett, C.R.
History
DepositionSep 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane regulatory protein ToxS
B: Transmembrane regulatory protein ToxS


Theoretical massNumber of molelcules
Total (without water)33,6862
Polymers33,6862
Non-polymers00
Water1,60389
1
A: Transmembrane regulatory protein ToxS


Theoretical massNumber of molelcules
Total (without water)16,8431
Polymers16,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transmembrane regulatory protein ToxS


Theoretical massNumber of molelcules
Total (without water)16,8431
Polymers16,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.850, 58.330, 89.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Transmembrane regulatory protein ToxS


Mass: 16842.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: toxS / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): CodonPlus / References: UniProt: Q05939
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM Hepes free acid, Sodium hydroxide pH 7.5, 200 mM Sodium malonate dibasic pH 7.0, 20% (w/v) PEG 2000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920112 Å / Relative weight: 1
ReflectionResolution: 2→26.93 Å / Num. obs: 19563 / % possible obs: 99.84 % / Redundancy: 8.8 % / Biso Wilson estimate: 43.25 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1035 / Rrim(I) all: 0.1102 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.076 Å / Num. unique obs: 1912 / CC1/2: 0.548 / CC star: 0.841

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.93 Å / SU ML: 0.3177 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2507
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2634 1958 10.01 %
Rwork0.2076 17593 -
obs0.2133 19551 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.45 Å2
Refinement stepCycle: LAST / Resolution: 2→26.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 0 89 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732223
X-RAY DIFFRACTIONf_angle_d0.92772998
X-RAY DIFFRACTIONf_chiral_restr0.0586358
X-RAY DIFFRACTIONf_plane_restr0.0059379
X-RAY DIFFRACTIONf_dihedral_angle_d12.8788835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35441320.30761223X-RAY DIFFRACTION99.71
2.05-2.110.31481170.2661243X-RAY DIFFRACTION99.78
2.11-2.170.37241590.24711234X-RAY DIFFRACTION100
2.17-2.240.33631260.23881241X-RAY DIFFRACTION99.85
2.24-2.320.3061560.23611208X-RAY DIFFRACTION99.78
2.32-2.410.32041310.22191259X-RAY DIFFRACTION99.86
2.41-2.520.32261350.22291238X-RAY DIFFRACTION100
2.52-2.660.31171430.22111260X-RAY DIFFRACTION99.79
2.66-2.820.26431330.20921242X-RAY DIFFRACTION99.85
2.82-3.040.28381440.20461251X-RAY DIFFRACTION99.93
3.04-3.350.231390.19211271X-RAY DIFFRACTION99.93
3.35-3.830.26391440.18381272X-RAY DIFFRACTION100
3.83-4.820.20751410.17681288X-RAY DIFFRACTION100
4.82-26.930.26191580.22811363X-RAY DIFFRACTION100

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