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- PDB-6j8l: Phytophthora sojae effector PsAvh240 inhibits a host aspartic pro... -

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Basic information

Entry
Database: PDB / ID: 6j8l
TitlePhytophthora sojae effector PsAvh240 inhibits a host aspartic protease secretion to promote infection
ComponentsAvh240
KeywordsIMMUNE SYSTEM / apoplastic immunity / effector / aspartic protease
Function / homologyhost cell plasma membrane / extracellular region / membrane / RxLR effector protein Avh240
Function and homology information
Biological speciesPhytophthora sojae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsGuo, B.
CitationJournal: Mol Plant / Year: 2019
Title: Phytophthora sojae Effector PsAvh240 Inhibits Host Aspartic Protease Secretion to Promote Infection.
Authors: Guo, B. / Wang, H. / Yang, B. / Jiang, W. / Jing, M. / Li, H. / Xia, Y. / Xu, Y. / Hu, Q. / Wang, F. / Yu, F. / Wang, Y. / Ye, W. / Dong, S. / Xing, W. / Wang, Y.
History
DepositionJan 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avh240
B: Avh240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,58910
Polymers31,8212
Non-polymers7698
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-97 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.350, 65.679, 143.199
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Avh240


Mass: 15910.333 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora sojae (eukaryote) / Gene: Avh / Production host: Escherichia coli (E. coli) / References: UniProt: E0W4T1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4
Details: 20% PEG3350, 0.1 M sodium acetate (pH 4.0), and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15483 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 53.39 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.046 / Rrim(I) all: 0.116 / Χ2: 0.968 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.345.40.87820.7170.3760.8930.50699.7
2.34-2.386.30.8977290.8170.3850.9780.5199.7
2.38-2.436.60.8287520.8340.3480.90.52499.9
2.43-2.486.70.6757510.8270.2810.7320.54299.9
2.48-2.536.50.5517790.8810.2320.5990.55699.9
2.53-2.596.50.5287350.8870.2230.5740.56599.9
2.59-2.666.40.4417580.8970.1880.4810.64299.5
2.66-2.736.30.3647730.930.1570.3970.67499.6
2.73-2.815.90.2977320.9420.1310.3260.81399.6
2.81-2.96.20.2387820.9730.1030.260.8199.5
2.9-36.70.2147650.9720.0890.2320.88499.2
3-3.126.60.1787660.9780.0740.1931.08999.9
3.12-3.266.50.1577620.9870.0670.1711.08999.9
3.26-3.446.40.1257800.990.0540.1371.486100
3.44-3.655.90.1097750.9920.0480.121.55999.9
3.65-3.936.30.0927930.9940.040.11.5499.9
3.93-4.336.60.0837780.9920.0360.0911.564100
4.33-4.956.30.0728000.9950.0320.0791.314100
4.95-6.245.90.0668050.9940.030.0731.02799.5
6.24-105.70.0698810.9960.0310.0761.5599.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→34.32 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.2516 791 5.11 %
Rwork0.2108 --
obs0.213 15483 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.42 Å2 / Biso mean: 64.2808 Å2 / Biso min: 34.56 Å2
Refinement stepCycle: final / Resolution: 2.3→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 40 61 2269
Biso mean--99.62 56.14 -
Num. residues----264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.44410.35061070.261124052512
2.4441-2.63270.33731500.276423812531
2.6327-2.89750.28421180.269424252543
2.8975-3.31650.36251420.262324122554
3.3165-4.17730.23381180.195524792597
4.1773-34.32360.19771560.175325902746
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.3005-1.12691.10035.9305-3.04455.39930.01220.08850.26480.450.19660.1794-0.1581-0.2046-0.18620.4005-0.00010.14170.45490.01760.40365.08259.7499176.2937
22.92352.21731.53784.8065-1.59946.05480.49360.15360.0585-0.9062-0.0315-0.70540.11380.7555-0.44560.87310.01770.26320.6209-0.14650.576628.2378-2.3384145.7925
33.0021-1.3085-2.20862.14271.5073.74050.1174-0.26380.1664-0.25750.1424-0.3022-0.00820.4965-0.29670.47110.02240.10560.5303-0.04840.409317.00356.2733162.6326
44.1712.95082.29575.06251.89293.8548-0.0429-0.28850.0340.304-0.0754-0.1637-0.0544-0.1550.05030.58140.02840.14590.4460.05170.4484-7.5302-2.702201.5182
53.2327-0.0258-0.43054.9386-0.7311.12450.0580.11910.15540.2983-0.05490.08680.0204-0.2946-0.00650.45610.01130.12270.45980.01610.3032-7.2834.5978190.5501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 133 )A59 - 133
2X-RAY DIFFRACTION3chain 'B' and (resid 59 through 133 )B59 - 133

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