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Yorodumi- PDB-5mpy: Crystal structure of Arabidopsis thaliana RNA editing factor MORF9 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mpy | ||||||
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Title | Crystal structure of Arabidopsis thaliana RNA editing factor MORF9 | ||||||
Components | Multiple organellar RNA editing factor 9, chloroplastic | ||||||
Keywords | PLANT PROTEIN / NFLD-related fold | ||||||
Function / homology | Function and homology information chloroplast RNA modification / cytidine to uridine editing / chloroplast envelope / chloroplast stroma / chloroplast / mRNA processing / protein dimerization activity / mRNA binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.247 Å | ||||||
Authors | Haag, S. / Schindler, M. / Berndt, L. / Brennicke, A. / Takenaka, M. / Weber, G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Crystal structures of the Arabidopsis thaliana organellar RNA editing factors MORF1 and MORF9. Authors: Haag, S. / Schindler, M. / Berndt, L. / Brennicke, A. / Takenaka, M. / Weber, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mpy.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mpy.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/5mpy ftp://data.pdbj.org/pub/pdb/validation_reports/mp/5mpy | HTTPS FTP |
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-Related structure data
Related structure data | 5mpwSC 5mpxC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 11535.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MORF9, RIP9, At1g11430, T23J18.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LPZ1 #2: Chemical | ChemComp-CA / #3: 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: 4.52 Å3/Da / Density % sol: 72.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.08 M sodium cacodylate, pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol, 0.16 M calcium acetate and 0.04 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.247→50 Å / Num. obs: 21313 / % possible obs: 99.6 % / Redundancy: 10.5 % / Rsym value: 0.09 / Net I/σ(I): 16.99 |
Reflection shell | Resolution: 2.25→2.38 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.56 / Num. unique all: 3327 / CC1/2: 0.772 / Rsym value: 1.42 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MPW Resolution: 2.247→46.016 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.82 Å2 / Biso mean: 59.7022 Å2 / Biso min: 29.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.247→46.016 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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