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Yorodumi- PDB-6fmb: Crystal structure of the BEC1054 RNase-like effector from the fun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fmb | ||||||
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Title | Crystal structure of the BEC1054 RNase-like effector from the fungal pathogen Blumeria graminis | ||||||
Components | CSEP0064 putative effector protein | ||||||
Keywords | RNA BINDING PROTEIN / Blumeria graminis / effector / CSEP0064/BEC1054 / RIP / Bimolecular Fluorescence Complementation / split YFP / RALPH / RNA-binding protein / RNase structure / fungal pathogen | ||||||
Function / homology | host cell / : / extracellular region / Secreted effector CSEP0064 Function and homology information | ||||||
Biological species | Blumeria graminis f. sp. hordei (grass mildew) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å | ||||||
Authors | Jones, R. / Garnett, J. / Spanu, P.D. / Cota, E. | ||||||
Citation | Journal: Biorxiv / Year: 2018 Title: Crystal structure of the BEC1054 RNase-like effector from the fungal pathogen Blumeria graminis Authors: Jones, R. / Garnett, J. / Spanu, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fmb.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fmb.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fmb ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fmb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10781.907 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blumeria graminis f. sp. hordei (grass mildew) Gene: BGHDH14_bgh02874 / Production host: Escherichia coli (E. coli) / References: UniProt: N1JJ94 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Purified CSEP0064/BEC1054 was dialysed into crystallisation buffer (10 mM Tris, 150 mM NaCl, pH 7.0) and concentrated to 10 mg/ml for crystallisation. Commercially available solution ...Details: Purified CSEP0064/BEC1054 was dialysed into crystallisation buffer (10 mM Tris, 150 mM NaCl, pH 7.0) and concentrated to 10 mg/ml for crystallisation. Commercially available solution conditions for crystallisation (Hampton Research,CA, USA) were screened. The protein was combined with the mother liquor on a 1:1 ratio in 200 nl drops. Crystals obtained in 0.1 M sodium acetate buffer pH 5.0, supplemented with 30% PEG 4000, 0.4 M (NH4)2SO4 were cryoprotected with 30% glycerol and flash frozen for data collection. |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92, 0.95 | |||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 1, 2015 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.3→52.51 Å / Num. obs: 21286 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 0.998 / Net I/σ(I): 23.4 | |||||||||
Reflection shell | Resolution: 1.3→1.34 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 1483 / CC1/2: 0.996 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.3→52.41 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.469 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.049 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.399 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→52.41 Å
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Refine LS restraints |
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