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- PDB-7f3i: Crystal structure of human YBX2 CSD in complex with m5C RNA in sp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f3i | ||||||
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Title | Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121 | ||||||
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![]() | RNA BINDING PROTEIN/RNA / Complex / protein-RNA / YBX / Cold-shock domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | ![]() translational attenuation / oocyte development / positive regulation of cold-induced thermogenesis / spermatogenesis / regulation of gene expression / transcription by RNA polymerase II / nucleic acid binding / DNA binding / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Huang, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121 Authors: Zhang, Y. / Huang, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.9 KB | Display | ![]() |
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PDB format | ![]() | 54.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.7 KB | Display | ![]() |
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Full document | ![]() | 474.7 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a6jS S: Starting model for refinement |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 10205.441 Da / Num. of mol.: 3 / Mutation: I92T, Q93K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: RNA chain | Mass: 1550.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.47 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Imidazole, 20% (w/v) PEG 8000, 3% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 15180 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 29.94 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.25→2.29 Å / Rmerge(I) obs: 0.477 / Num. unique obs: 757 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6A6J Resolution: 2.25→29.67 Å / SU ML: 0.2372 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.3658 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: 31.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→29.67 Å
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Refine LS restraints |
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LS refinement shell |
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