+Open data
-Basic information
Entry | Database: PDB / ID: 5gi0 | ||||||
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Title | Crystal structure of RNA editing factor MORF9/RIP9 | ||||||
Components | Multiple organellar RNA editing factor 9, chloroplastic | ||||||
Keywords | RNA BINDING PROTEIN / RNA editing factor / MORF9 / RIP9 | ||||||
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 / SAD / Resolution: 2.044 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 | 5gi0.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gi0.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gi0_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 5gi0_full_validation.pdf.gz | 426.1 KB | Display | |
Data in XML | 5gi0_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 5gi0_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/5gi0 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/5gi0 | 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: 15734.685 Da / Num. of mol.: 1 / Mutation: C13S, C115S 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LPZ1 |
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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: 2.35 Å3/Da / Density % sol: 47.58 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: sodium bromide,sodium thiocyanate, PEG 3350, MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979305 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979305 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. obs: 9121 / % possible obs: 99.47 % / Redundancy: 8.9 % / Net I/σ(I): 32.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.044→29.87 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.044→29.87 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: 10.8742 Å / Origin y: 35.2392 Å / Origin z: 12.4412 Å
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Refinement TLS group | Selection details: all |