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- PDB-7xp9: Phytophthora infesfans RxLR effector AVRvnt1 -

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Basic information

Entry
Database: PDB / ID: 7xp9
TitlePhytophthora infesfans RxLR effector AVRvnt1
ComponentsRxLR effector protein Avr-vnt11
KeywordsIMMUNE SYSTEM / RxLR effector / triggered plant immunity response
Function / homologyhost cell nucleolus / host cell cytoplasm / extracellular region / RxLR effector protein Avr-vnt11
Function and homology information
Biological speciesPhytophthora infestans T30-4 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsXing, W. / Hu, Q. / Zhou, J. / Yao, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Chloroplast Protein GLYK Hijacked by Phytophthora Infestans Effector AVRvnt1 in Cytoplasm to Activate NLR
Authors: Xing, W. / Hu, Q. / Zhou, J. / Yao, D.
History
DepositionMay 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 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: RxLR effector protein Avr-vnt11


Theoretical massNumber of molelcules
Total (without water)9,5811
Polymers9,5811
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5400 Å2
Unit cell
Length a, b, c (Å)54.004, 54.004, 116.547
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein RxLR effector protein Avr-vnt11 / Avirulence protein Avr-vnt1


Mass: 9581.048 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora infestans T30-4 (eukaryote)
Strain: T30-4 / Gene: Avr-vnt1, PITG_16294 / Production host: Escherichia coli (E. coli) / References: UniProt: D0NTY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% w/v Polyethylene glycol 3,350, 0.1 M Bis-Tris pH 5.5 and 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 14032 / % possible obs: 96.9 % / Redundancy: 40.2 % / Biso Wilson estimate: 27.46 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.01 / Rrim(I) all: 0.059 / Χ2: 2.945 / Net I/σ(I): 23.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.9641.40.1653640.9970.0260.1671.87795.8
1.96-243.10.1433870.9980.0220.1452.05796.3
2-2.0442.10.133690.9980.020.1322.29896.6
2.04-2.0841.90.1183900.9990.0180.1192.43396.1
2.08-2.1242.20.1053700.9990.0160.1072.52896.6
2.12-2.1742.30.13900.9990.0150.1012.62496.8
2.17-2.2341.50.0913770.9990.0140.0922.74896.9
2.23-2.2941.70.0833830.9990.0130.0842.8196.5
2.29-2.3641.70.0783890.9990.0120.0792.81297.2
2.36-2.4341.50.0763800.9990.0120.0772.83196.7
2.43-2.5240.90.0723910.9990.0120.0733.01798
2.52-2.62410.073940.9990.0110.0712.9497
2.62-2.74410.0664050.9990.010.0673.01797.8
2.74-2.88410.06239010.010.0633.24997.7
2.88-3.0639.60.05740310.0090.0583.37297.3
3.06-3.339.90.05539810.0090.0563.34798
3.3-3.6338.40.0544170.9990.0090.0553.69798.3
3.63-4.1637.80.0524200.9990.0080.0523.73398.1
4.16-5.2435.80.04842510.0080.0493.51897.7
5.24-5031.30.054660.9990.0090.0514.11292.6
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→36.47 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 1407 10.03 %
Rwork0.2222 12625 -
obs0.2263 14032 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.81 Å2 / Biso mean: 27.2077 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: final / Resolution: 1.93→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms613 0 0 50 663
Biso mean---28.93 -
Num. residues----76
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-20.32221430.25971248139197
2-2.080.28811350.22561254138997
2.08-2.170.23961420.22171254139698
2.17-2.290.24851420.23181245138798
2.29-2.430.26961340.23081261139598
2.43-2.620.34451420.25261271141399
2.62-2.880.30841480.25671270141899
2.88-3.30.27641360.21931276141299
3.3-4.150.21021470.19561284143199
4.16-36.470.25071380.211262140098

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