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- PDB-8bd1: Crystal structure of the RhsPWHH-RhsPI toxin-immunity pair -

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Basic information

Entry
Database: PDB / ID: 8bd1
TitleCrystal structure of the RhsPWHH-RhsPI toxin-immunity pair
Components
  • SMI1/KNR4 family protein
  • Type IV secretion protein Rhs
KeywordsTOXIN / Vibrio parahaemolyticus / Type-VI secretion system effector / Rhs toxin / WHH domain
Function / homologyWHH domain-containing protein / A nuclease of the HNH/ENDO VII superfamily with conserved WHH / Knr4/Smi1-like domain superfamily / RHS protein / RHS protein / Rhs repeat-associated core / : / SMI1/KNR4 family protein / Type IV secretion protein Rhs
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.26 Å
AuthorsChao, W.C.H. / Wu, H.W. / Li, H.
Funding supportMacao, 3items
OrganizationGrant numberCountry
Other governmentMYRG2018-00221-FHSMacao
Other government0009/2018/A1Macao
Other government0032/2021/A1Macao
CitationJournal: To Be Published
Title: Crystal structure of the RhsPWHH-RhsPI toxin-immunity pair
Authors: Chao, W.C.H.
History
DepositionOct 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 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: Type IV secretion protein Rhs
B: SMI1/KNR4 family protein


Theoretical massNumber of molelcules
Total (without water)29,9682
Polymers29,9682
Non-polymers00
Water4,576254
1
A: Type IV secretion protein Rhs
B: SMI1/KNR4 family protein

A: Type IV secretion protein Rhs
B: SMI1/KNR4 family protein


Theoretical massNumber of molelcules
Total (without water)59,9364
Polymers59,9364
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
Buried area7000 Å2
ΔGint-29 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.580, 51.580, 206.140
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
Components on special symmetry positions
IDModelComponents
11A-1498-

HOH

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Components

#1: Protein Type IV secretion protein Rhs / RhsPWHH


Mass: 14725.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: CA163_08985 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A227JDU1
#2: Protein SMI1/KNR4 family protein / RhsPI


Mass: 15242.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: CA163_08980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8UU71
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.4M potassium sodium tartrate and 19% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.26→25.79 Å / Num. obs: 76480 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 18.53 Å2 / CC1/2: 1 / Net I/σ(I): 22.38
Reflection shellResolution: 1.26→1.31 Å / Num. unique obs: 7488 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.26→25.79 Å / SU ML: 0.132 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 3907 5.11 %
Rwork0.1979 72573 -
obs0.1989 76480 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.45 Å2
Refinement stepCycle: LAST / Resolution: 1.26→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 0 254 2285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482078
X-RAY DIFFRACTIONf_angle_d0.76612812
X-RAY DIFFRACTIONf_chiral_restr0.0831308
X-RAY DIFFRACTIONf_plane_restr0.0044362
X-RAY DIFFRACTIONf_dihedral_angle_d5.8689272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.31871370.28592509X-RAY DIFFRACTION99.96
1.28-1.290.29241360.26412563X-RAY DIFFRACTION100
1.29-1.310.27451300.25272546X-RAY DIFFRACTION99.96
1.31-1.330.27171420.24222575X-RAY DIFFRACTION100
1.33-1.350.25811490.24252480X-RAY DIFFRACTION99.96
1.35-1.370.23581600.23612550X-RAY DIFFRACTION100
1.37-1.390.26811310.23782540X-RAY DIFFRACTION100
1.39-1.410.26171430.22852559X-RAY DIFFRACTION99.96
1.41-1.430.27331670.23042535X-RAY DIFFRACTION100
1.43-1.460.2751560.22242552X-RAY DIFFRACTION99.89
1.46-1.490.23731220.22422560X-RAY DIFFRACTION100
1.49-1.520.2511270.21992606X-RAY DIFFRACTION99.96
1.52-1.550.21521390.21042533X-RAY DIFFRACTION99.96
1.55-1.590.21591470.20812528X-RAY DIFFRACTION99.96
1.59-1.630.23851260.20542580X-RAY DIFFRACTION99.96
1.63-1.670.23711390.20112595X-RAY DIFFRACTION99.96
1.67-1.720.23661280.22601X-RAY DIFFRACTION100
1.72-1.780.18611480.20072569X-RAY DIFFRACTION100
1.78-1.840.23751340.2022577X-RAY DIFFRACTION100
1.84-1.910.23441240.20242605X-RAY DIFFRACTION100
1.91-20.21011300.2052599X-RAY DIFFRACTION99.93
2-2.110.21671300.20242620X-RAY DIFFRACTION100
2.11-2.240.22431430.19042616X-RAY DIFFRACTION99.96
2.24-2.410.21861340.19632634X-RAY DIFFRACTION100
2.41-2.650.19361690.20692610X-RAY DIFFRACTION100
2.65-3.030.18651310.20412726X-RAY DIFFRACTION99.97
3.04-3.820.20521370.18222697X-RAY DIFFRACTION100
3.82-25.790.22821480.17852908X-RAY DIFFRACTION99.77

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