+Open data
-Basic information
Entry | Database: PDB / ID: 6l8k | ||||||
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Title | Structure of URT1 in complex with UTP | ||||||
Components | UTP:RNA uridylyltransferase 1RNA uridylyltransferase | ||||||
Keywords | TRANSFERASE / Uridylyltransferase / Complex | ||||||
Function / homology | Function and homology information negative regulation of post-transcriptional gene silencing by regulatory ncRNA / miRNA catabolic process / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / nuclear-transcribed mRNA poly(A) tail shortening / P-body / mRNA processing / mRNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.999 Å | ||||||
Authors | Lingru, Z. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Crystal structure of Arabidopsis terminal uridylyl transferase URT1. Authors: Zhu, L. / Hu, Q. / Cheng, L. / Jiang, Y. / Lv, M. / Liu, Y. / Li, F. / Shi, Y. / Gong, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l8k.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l8k.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 6l8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/6l8k ftp://data.pdbj.org/pub/pdb/validation_reports/l8/6l8k | HTTPS FTP |
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-Related structure data
Related structure data | 6l3fC 5w0nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43406.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: URT1, At2g45620, F17K2.15 / Production host: Escherichia coli (E. coli) / References: UniProt: O64642, RNA uridylyltransferase |
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#2: Chemical | ChemComp-UTP / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES PH7.5, 10% PEG6000, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.999→30.627 Å / Num. obs: 8925 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 65.73 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.857 |
Reflection shell | Resolution: 2.999→3.4 Å / Rmerge(I) obs: 0.499 / Num. unique obs: 2924 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5w0n Resolution: 2.999→30.627 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 24.89 / 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 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.39 Å2 / Biso mean: 61.8459 Å2 / Biso min: 27.94 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.999→30.627 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 25.761 Å / Origin y: -0.8185 Å / Origin z: 18.1913 Å
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Refinement TLS group |
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