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- PDB-5i9h: Crystal structure of designed pentatricopeptide repeat protein dP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i9h | ||||||
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Title | Crystal structure of designed pentatricopeptide repeat protein dPPR-U8G2 in complex with its target RNA U8G2 | ||||||
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![]() | RNA BINDING PROTEIN/RNA / single-stranded RNA / designer pentatricopeptide repeat protein / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | unidentified (others) synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shen, C. / Zhang, D. / Guan, Z. / Zou, T. / Yin, P. | ||||||
![]() | ![]() Title: Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins. Authors: Shen, C. / Zhang, D. / Guan, Z. / Liu, Y. / Yang, Z. / Yang, Y. / Wang, X. / Wang, Q. / Zhang, Q. / Fan, S. / Zou, T. / Yin, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.2 KB | Display | ![]() |
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PDB format | ![]() | 133.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.6 KB | Display | ![]() |
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Full document | ![]() | 470.7 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i9dC ![]() 5i9fC ![]() 5i9gC ![]() 4pjrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51492.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: ![]() ![]() |
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#2: RNA chain | Mass: 5696.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PEG 3350, Bis-Tris propane, Magnesium chloride, Ethyl Acetate, D-(+)-glucose monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 15179 / % possible obs: 99.8 % / Redundancy: 10.1 % / Net I/σ(I): 19.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PJR Resolution: 2.504→47.699 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.29 / 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: 2.504→47.699 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: -10.4241 Å / Origin y: 1.0422 Å / Origin z: 19.6977 Å
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Refinement TLS group | Selection details: all |