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Yorodumi- PDB-2ikf: Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ikf | ||||||
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Title | Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP | ||||||
Components | RNA uridylyl transferase | ||||||
Keywords | TRANSFERASE / TUTase / Trypanosoma / nucleotidyltransferase / UTP-binding / RNA editing | ||||||
Function / homology | Function and homology information RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / kinetoplast / nucleotide binding / mitochondrion / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Luecke, H. / Stagno, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: UTP-bound and Apo Structures of a Minimal RNA Uridylyltransferase. Authors: Stagno, J. / Aphasizheva, I. / Rosengarth, A. / Luecke, H. / Aphasizhev, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ikf.cif.gz | 144.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ikf.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ikf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/2ikf ftp://data.pdbj.org/pub/pdb/validation_reports/ik/2ikf | HTTPS FTP |
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-Related structure data
Related structure data | 2nomC 2b51S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39879.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: 841358, Tb11.01.7300 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q381M1, RNA uridylyltransferase #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-UTP / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 18% PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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→103.407 Å / Num. obs: 43289 / % possible obs: 94.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 6.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2B51 Resolution: 2→51.709 Å / σ(F): 0
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Solvent computation | Bsol: 48.943 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.984 Å2
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Refinement step | Cycle: LAST / Resolution: 2→51.709 Å
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Refine LS restraints |
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Xplor file |
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