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- PDB-8gug: Structure of VPA0770 toxin bound to VPA0769 antitoxin in Vibrio p... -

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Basic information

Entry
Database: PDB / ID: 8gug
TitleStructure of VPA0770 toxin bound to VPA0769 antitoxin in Vibrio parahaemolyticus
Components
  • DUF2384 domain-containing protein
  • RES domain-containing protein
KeywordsTOXIN / Complex / Antitoxin
Function / homology
Function and homology information


Antitoxin Xre / Antitoxin Xre-like, helix-turn-helix domain / Antitoxin Xre-like helix-turn-helix domain / Antitoxin Xre/MbcA/ParS-like, toxin-binding domain / Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain / RES domain / RES domain / RES
Similarity search - Domain/homology
RES domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus serotype O3:K6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSong, X.J. / Zhang, Y. / Xu, Y.Y. / Lin, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21974093 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural insights of the toxin-antitoxin system VPA0770-VPA0769 in Vibrio parahaemolyticus.
Authors: Zhang, Y. / Song, X. / Chen, C. / Liu, L. / Xu, Y. / Zhang, N. / Huang, W. / Zheng, J. / Yuan, W. / Tang, L. / Lin, Z.
History
DepositionSep 12, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RES domain-containing protein
B: DUF2384 domain-containing protein
C: DUF2384 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)52,7323
Polymers52,7323
Non-polymers00
Water1,11762
1
A: RES domain-containing protein
B: DUF2384 domain-containing protein
C: DUF2384 domain-containing protein

A: RES domain-containing protein
B: DUF2384 domain-containing protein
C: DUF2384 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)105,4656
Polymers105,4656
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area11280 Å2
ΔGint-42 kcal/mol
Surface area37300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.915, 104.725, 116.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

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Components

#1: Protein RES domain-containing protein


Mass: 18040.590 Da / Num. of mol.: 1 / Mutation: G26K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Gene: VPA0770 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q87I36
#2: Protein DUF2384 domain-containing protein / VPA0769 antitoxin


Mass: 17345.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Gene: VPA0769 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q87I37
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 48.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium chloride dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.84→36.333 Å / Num. obs: 11673 / % possible obs: 96.77 % / Redundancy: 7.4 % / Biso Wilson estimate: 75.35 Å2 / Rrim(I) all: 0.142 / Net I/σ(I): 15.8
Reflection shellResolution: 2.84→2.93 Å / Redundancy: 4.4 % / Num. unique obs: 861 / Rrim(I) all: 0.722 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Predicted model

Resolution: 2.85→33.48 Å / SU ML: 0.4094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2744 588 5.06 %
Rwork0.2473 11039 -
obs0.2487 11627 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.72 Å2
Refinement stepCycle: LAST / Resolution: 2.85→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 0 67 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273396
X-RAY DIFFRACTIONf_angle_d0.51924583
X-RAY DIFFRACTIONf_chiral_restr0.0371508
X-RAY DIFFRACTIONf_plane_restr0.0038593
X-RAY DIFFRACTIONf_dihedral_angle_d20.96611299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.130.32771290.2772424X-RAY DIFFRACTION86.78
3.13-3.580.28881520.24312802X-RAY DIFFRACTION99.16
3.58-4.510.27171460.22742849X-RAY DIFFRACTION99.87
4.51-33.480.2621610.25552964X-RAY DIFFRACTION99.84

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