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Yorodumi- PDB-5izw: Crystal structure of RNA editing specific factor of designer PLS-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5izw | ||||||
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Title | Crystal structure of RNA editing specific factor of designer PLS-type PPR-9R protein | ||||||
Components | PLS9-PPR | ||||||
Keywords | RNA BINDING PROTEIN / pentatricopeptide repeat / complex / MORF | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.738 Å | ||||||
Authors | Yan, J. / Zhang, Q. / Guan, Z. / Zou, T. / Yin, P. | ||||||
Citation | Journal: Nat Plants / Year: 2017 Title: MORF9 increases the RNA-binding activity of PLS-type pentatricopeptide repeat protein in plastid RNA editing Authors: Yan, J. / Zhang, Q. / Guan, Z. / Wang, Q. / Li, L. / Ruan, F. / Lin, R. / Zou, T. / Yin, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5izw.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5izw.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 5izw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/5izw ftp://data.pdbj.org/pub/pdb/validation_reports/iz/5izw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11267.071 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 57.01 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: Magnesium sulfate heptahydrate, 1,3-Bis[tris(hydroxymethyl)methylamino]propane, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.738→45 Å / Num. obs: 26305 / % possible obs: 99.9 % / Redundancy: 13.4 % / Net I/σ(I): 24.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.738→36.501 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75 / 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: 1.738→36.501 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.6247 Å / Origin y: 116.7232 Å / Origin z: 7.9213 Å
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Refinement TLS group | Selection details: all |