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- PDB-8igd: The crystal structure of the minimal interaction domains of DRB7.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8igd | ||||||
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Title | The crystal structure of the minimal interaction domains of DRB7.2:DRB4 complex | ||||||
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![]() | GENE REGULATION / Double stranded RNA Binding proteins (dsRBPs) | ||||||
Function / homology | ![]() ta-siRNA processing / RNAi-mediated antiviral immune response / miRNA processing / double-stranded RNA binding / defense response to virus / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Paturi, S. / Deshmukh, M.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The mechanism of the DRB7.2:DRB4 mediated endogenous inverted-repeat dsRNA (endo-IR dsRNA) sequestering in plants Authors: Paturi, S. / Deshmukh, M.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.4 KB | Display | ![]() |
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PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.8 KB | Display | ![]() |
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Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i8v ![]() 8i8w |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 11002.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 8268.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % Description: Diamond shaped crystals were formed within 3 days of crystallisation setup. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, sodium citrate tribasic dihydrate, and isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford cryostream controller 700 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 14, 2019 / Details: VariMax HF |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.95 Å / Num. obs: 9938 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 62.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.026 / Rrim(I) all: 0.073 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.9→3.04 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.418 / Num. unique obs: 4256 / CC1/2: 0.93 / Rpim(I) all: 0.161 / Rrim(I) all: 0.448 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.05 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→29.95 Å
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Refine LS restraints |
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LS refinement shell |
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