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- PDB-5a6w: 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: 5a6w | ||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikp1 from rice (Oryza sativa) | ||||||
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![]() | ANTIVIRAL PROTEIN / RICE BLAST DISEASE / PLANT DISEASE RESISTANCE / EFFECTOR PROTEIN / INTEGRATED HMA DOMAIN | ||||||
Function / homology | ![]() defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maqbool, A. / Saitoh, H. / Franceschetti, M. / Stevenson, C.E. / Uemura, A. / Kanzaki, H. / Kamoun, S. / Terauchi, R. / Banfield, M.J. | ||||||
![]() | ![]() Title: Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor. Authors: Maqbool, A. / Saitoh, H. / Franceschetti, M. / Stevenson, C.E. / Uemura, A. / Kanzaki, H. / Kamoun, S. / Terauchi, R. / Banfield, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.2 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.1 KB | Display | ![]() |
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Full document | ![]() | 464.1 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a6pSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7816.232 Da / Num. of mol.: 2 / Fragment: PIKP-HMA, UNP RESIDUES 186-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 10827.340 Da / Num. of mol.: 1 / Fragment: AVR-PIKD, UNP RESIDUES 22-113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Details: 2M AMMONIUM SULPHATE, 0.1M CHES PH 9 AND 20% PEG335 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39.47 Å / Num. obs: 32549 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 17.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5A6P Resolution: 1.6→39.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.627 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.154 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→39.47 Å
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Refine LS restraints |
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