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Open data
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Basic information
Entry | Database: PDB / ID: 7sos | ||||||
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Title | LaM domain of human LARP1 in complex with AAAA RNA | ||||||
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![]() | RNA BINDING PROTEIN/RNA / Winged helix fold / RNA binding domain / ![]() | ||||||
Function / homology | : / ![]() ![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kozlov, G. / Gehring, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of 3'-end poly(A) RNA recognition by LARP1. Authors: Kozlov, G. / Mattijssen, S. / Jiang, J. / Nyandwi, S. / Sprules, T. / Iben, J.R. / Coon, S.L. / Gaidamakov, S. / Noronha, A.M. / Wilds, C.J. / Maraia, R.J. / Gehring, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.7 KB | Display | ![]() |
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PDB format | ![]() | 40.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sooSC ![]() 7sopC ![]() 7soqC ![]() 7sorC ![]() 7sotC ![]() 7souC ![]() 7sovC S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 11806.507 Da / Num. of mol.: 1 / Fragment: Residues 323-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.07 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.08M magnesium acetate, 1.344M potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.25→50 Å / Num. obs: 28289 / % possible obs: 97.7 % / Redundancy: 7 % / Biso Wilson estimate: 16.28 Å2 / Rsym value: 0.039 / Net I/σ(I): 50.4 |
Reflection shell | Resolution: 1.25→1.27 Å / Num. unique obs: 2236 / Rsym value: 0.464 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7SOO Resolution: 1.25→36.6 Å / SU ML: 0.1478 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.121 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: 22.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→36.6 Å
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Refine LS restraints |
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LS refinement shell |
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