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Yorodumi- PDB-3zrg: Crystal structure of RxLR effector PexRD2 from Phytophthora infestans -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zrg | ||||||
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Title | Crystal structure of RxLR effector PexRD2 from Phytophthora infestans | ||||||
Components | PEXRD2 FAMILY SECRETED RXLR EFFECTOR PEPTIDE, PUTATIVE | ||||||
Keywords | PROTEIN BINDING / PLANT PATHOGEN INTERACTIONS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PHYTOPHTHORA INFESTANS (potato late blight agent) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | King, S.R.F. / Boutemy, L.S. / Win, J. / Hughes, R.K. / Clarke, T.A. / Blumenschein, T.M.A. / Kamoun, S. / Banfield, M.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structures of Phytophthora Rxlr Effector Proteins: A Conserved But Adaptable Fold Underpins Functional Diversity. Authors: Boutemy, L.S. / King, S.R.F. / Win, J. / Hughes, R.K. / Clarke, T.A. / Blumenschein, T.M.A. / Kamoun, S. / Banfield, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zrg.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zrg.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zrg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zrg_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 3zrg_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 3zrg_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 3zrg_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/3zrg ftp://data.pdbj.org/pub/pdb/validation_reports/zr/3zrg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7355.747 Da / Num. of mol.: 2 / Fragment: EFFECTOR DOMAIN, RESIDUES 57-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PHYTOPHTHORA INFESTANS (potato late blight agent) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0NIL2, UniProt: D0NIN5*PLUS #2: Chemical | ChemComp-BR / #3: Water | ChemComp-HOH / | Sequence details | N-TERMINAL TWO RESIDUES ARE NON-NATIVE, AND DERIVED FROM THE PROTEASE CLEAVAGE SITE FOLLOWING ...N-TERMINAL TWO RESIDUES ARE NON-NATIVE, AND DERIVED FROM THE PROTEASE CLEAVAGE SITE FOLLOWING REMOVAL OF AFFINITY- TAG | |
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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: 2.14 Å3/Da / Density % sol: 42.43 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 2.6 M AMMONIUM SULPHATE, 0.1 M TRIS.HCL PH 7.5 AND 0.2 M AMMONIUM BROMIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→37.7 Å / Num. obs: 12601 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 9.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.75→37.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.049 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.145 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→37.7 Å
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Refine LS restraints |
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