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- PDB-9rsv: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9rsv | ||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-Pia with the HMA domain of OsHPP09 from rice (Oryza sativa) | ||||||
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![]() | PLANT PROTEIN / Effector / HMA | ||||||
Function / homology | : / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / metal ion binding / Os03g0111400 protein / AVR-Pia protein![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maidment, J.H.R. / Bocquet, A. / Gelin, M. / De Guillen, K. / Cesari, S. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: The Magnaporthe oryzae MAX effector AVR-Pia binds a novel group of rice HMA domain-containing proteins Authors: Maidment, J.H. / Saile, S.C. / Bocquet, A. / Thivolle, C. / Bourcet, L. / Planel, L.F. / Gelin, M. / Kroj, T. / Padilla, A. / de Guillen, K. / Cesari, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.3 KB | Display | ![]() |
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PDB format | ![]() | 51.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.1 KB | Display | ![]() |
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Full document | ![]() | 441.1 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 8080.542 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HMA domain / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 7788.915 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: No signal peptide. / Source: (gene. exp.) ![]() ![]() ![]() | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.911 Å3/Da / Density % sol: 57.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulphate, 20% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9655 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.83 Å / Num. obs: 23168 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.025 / Rrim(I) all: 0.044 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1125 / CC1/2: 0.837 / Rpim(I) all: 0.592 / Rrim(I) all: 1.059 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.032 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→46.83 Å
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Refine LS restraints |
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LS refinement shell |
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