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Open data
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Basic information
Entry | Database: PDB / ID: 7sot | ||||||
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Title | LaM domain of human LARP1 in complex with AAAAAA oligonucleotide | ||||||
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![]() | RNA BINDING PROTEIN/RNA / Winged helix fold / RNA binding domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | RNA / Isoform 2 of La-related protein 1![]() | ||||||
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 | ![]() | 69.4 KB | Display | ![]() |
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PDB format | ![]() | 40.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.2 KB | Display | ![]() |
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Full document | ![]() | 457.3 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sooSC ![]() 7sopC ![]() 7soqC ![]() 7sorC ![]() 7sosC ![]() 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: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 2 M ammonium sulfate |
-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: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. obs: 15675 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 20.92 Å2 / Rsym value: 0.039 / Net I/σ(I): 46.7 |
Reflection shell | Resolution: 1.52→1.56 Å / Num. unique obs: 1471 / Rsym value: 0.565 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7SOO Resolution: 1.52→36.37 Å / SU ML: 0.1952 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.0127 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: 27.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→36.37 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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