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- PDB-9ksg: Crystal structure of RxLR145 effector -

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Basic information

Entry
Database: PDB / ID: 9ksg
TitleCrystal structure of RxLR145 effector
ComponentsRXLR effector Avh1
KeywordsCYTOSOLIC PROTEIN / RxLR effector / nucleus and cytoplasm / UNKNOWN FUNCTION
Function / homology: / Effector PexRD54, WY-domain / host cell / extracellular region / RXLR effector Avh1
Function and homology information
Biological speciesPhytophthora capsici (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.577 Å
AuthorsZhang, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A Phytophthora effector ensures infection by initial suppression of pattern triggered immunity, and timed activation of pattern and effector triggered immunity
Authors: Zhang, X.G.
History
DepositionNov 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RXLR effector Avh1
B: RXLR effector Avh1


Theoretical massNumber of molelcules
Total (without water)110,2742
Polymers110,2742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.034, 89.587, 147.716
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RXLR effector Avh1


Mass: 55136.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora capsici (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A678WQQ4
Has ligand of interestN
Has protein modificationY

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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: 42.29 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.03M Citric acid, 0.07M BIS-TRIS propane pH 7.6, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.577→43.151 Å / Num. obs: 30135 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 37.73
Reflection shellResolution: 2.577→2.66 Å / Rmerge(I) obs: 0.464 / Num. unique obs: 30135

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.577→43.151 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.289 1982 6.58 %
Rwork0.2187 --
obs0.2233 30135 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.577→43.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6631 0 0 0 6631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126772
X-RAY DIFFRACTIONf_angle_d1.3949165
X-RAY DIFFRACTIONf_dihedral_angle_d16.8992541
X-RAY DIFFRACTIONf_chiral_restr0.0531033
X-RAY DIFFRACTIONf_plane_restr0.0071149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.577-2.64090.40461350.28351907X-RAY DIFFRACTION94
2.6409-2.71230.39541390.2621939X-RAY DIFFRACTION98
2.7123-2.79210.34651370.26261970X-RAY DIFFRACTION98
2.7921-2.88220.35261400.25481953X-RAY DIFFRACTION98
2.8822-2.98520.31531390.24891990X-RAY DIFFRACTION99
2.9852-3.10470.35941390.26222000X-RAY DIFFRACTION99
3.1047-3.2460.35611410.25182001X-RAY DIFFRACTION100
3.246-3.4170.31661410.23842014X-RAY DIFFRACTION100
3.417-3.6310.28881430.23172026X-RAY DIFFRACTION100
3.631-3.91120.29551430.20132046X-RAY DIFFRACTION100
3.9112-4.30450.27681420.19272023X-RAY DIFFRACTION100
4.3045-4.92660.21681460.18022065X-RAY DIFFRACTION100
4.9266-6.2040.23691460.21042079X-RAY DIFFRACTION100
6.204-43.1510.25591510.19552140X-RAY DIFFRACTION98

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