+Open data
-Basic information
Entry | Database: PDB / ID: 5z1v | ||||||
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Title | Crystal structure of AvrPib | ||||||
Components | AvrPib protein | ||||||
Keywords | UNKNOWN FUNCTION / Magnaporthe oryzae / MAX effector / protein crystal structure | ||||||
Function / homology | AvrPib protein Function and homology information | ||||||
Biological species | Magnaporthe oryzae (rice blast fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.661 Å | ||||||
Authors | Zhang, X. / He, D. / Zhao, Y.X. / Taylor, I.A. / Peng, Y.L. / Yang, J. / Liu, J.F. | ||||||
Citation | Journal: Plant J. / Year: 2018 Title: A positive-charged patch and stabilized hydrophobic core are essential for avirulence function of AvrPib in the rice blast fungus. Authors: Zhang, X. / He, D. / Zhao, Y. / Cheng, X. / Zhao, W. / Taylor, I.A. / Yang, J. / Liu, J. / Peng, Y.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z1v.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z1v.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 5z1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z1v_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 5z1v_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 5z1v_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 5z1v_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/5z1v ftp://data.pdbj.org/pub/pdb/validation_reports/z1/5z1v | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 7437.914 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AvrPib / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H4ITX1 #2: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.76 Å3/Da / Density % sol: 30.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium thiocyanate pH 6.9, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9776 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9776 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→42.45 Å / Num. obs: 24125 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.66→1.72 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.661→42.449 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 23.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.661→42.449 Å
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Refine LS restraints |
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LS refinement shell |
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