[English] 日本語
Yorodumi- PDB-5kal: Terminal uridylyl transferase 4 from Trypanosoma brucei with boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kal | ||||||
---|---|---|---|---|---|---|---|
Title | Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP and UpU | ||||||
Components |
| ||||||
Keywords | Transferase/RNA / trypanosoma / RNA editing / TUTase / transferase / Transferase-RNA complex | ||||||
Function / homology | Function and homology information RNA 3' uridylation / RNA 3'-end processing / RNA uridylyltransferase / RNA uridylyltransferase activity / kinetoplast / nucleotidyltransferase activity / nucleotide binding / mitochondrion / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Stagno, J.R. / Luecke, H. / Afasizhev, R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting. Authors: Rajappa-Titu, L. / Suematsu, T. / Munoz-Tello, P. / Long, M. / Demir, O. / Cheng, K.J. / Stagno, J.R. / Luecke, H. / Amaro, R.E. / Aphasizheva, I. / Aphasizhev, R. / Thore, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5kal.cif.gz | 400.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5kal.ent.gz | 331.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/5kal ftp://data.pdbj.org/pub/pdb/validation_reports/ka/5kal | HTTPS FTP |
---|
-Related structure data
Related structure data | 5hzdC 5i49C 5idoC 2ikfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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: TUT4 / Production host: Escherichia coli (E. coli) / References: UniProt: A4UBD5, UniProt: Q381M1*PLUS #2: RNA chain | Mass: 567.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Trypanosoma brucei (eukaryote) #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.42 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM sodium cacodylate pH 6.5, 200mM calcium acetate, 18% PEG-8000, 5mM UTP, 5mM UpU |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→47.13 Å / Num. obs: 20369 / % possible obs: 99.5 % / Redundancy: 3.52 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IKF Resolution: 2.75→47.129 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.35 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→47.129 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 23.1549 Å / Origin y: 26.5803 Å / Origin z: -69.644 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |