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Yorodumi- PDB-5iwb: Crystal structure of design pentatricopeptide repeat complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iwb | ||||||
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Title | Crystal structure of design pentatricopeptide repeat complex with MORF protein | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / pentatricopeptide repeat / complex / MORF | ||||||
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) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 Å | ||||||
Authors | Yan, J. / Zhang, Q. / Guan, Z. / Zou, T. / Yin, P. | ||||||
Citation | Journal: To be published Title: Structural basis for designer pentatricopeptide repeat proteins interaction with MORF protein Authors: Yan, J. / Zhang, Q. / Guan, Z. / 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 | 5iwb.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iwb.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 5iwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/5iwb ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iwb | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 15453.313 Da / Num. of mol.: 1 / Fragment: UNP residues 75-196 / Mutation: C12S, C114S 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: Protein | Mass: 14980.376 Da / Num. of mol.: 1 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) |
#3: 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: 2.23 Å3/Da / Density % sol: 44.84 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: Sodium cacodylate trihydrate,Magnesium acetate tetrahydrate,PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→45 Å / Num. obs: 28002 / % possible obs: 99.92 % / Redundancy: 27.6 % / Net I/σ(I): 40.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.764→42.41 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.19 / 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: 1.764→42.41 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: -18.5021 Å / Origin y: 11.7307 Å / Origin z: 5.1512 Å
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Refinement TLS group | Selection details: all |