[English] 日本語
Yorodumi- PDB-1xdn: High resolution crystal structure of an editosome enzyme from try... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xdn | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution crystal structure of an editosome enzyme from trypanosoma brucei: RNA editing ligase 1 | ||||||
Components | RNA editing ligase MP52 | ||||||
Keywords | LIGASE / RNA editing / Trypanosoma brucei | ||||||
Function / homology | Function and homology information RNA ligase (ATP) / RNA ligase (ATP) activity / RNA modification / mitochondrial mRNA editing complex / kinetoplast / mRNA processing / mitochondrion / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å | ||||||
Authors | Deng, J. / Schnaufer, A. / Salavati, R. / Stuart, K.D. / Hol, W.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. Authors: Deng, J. / Schnaufer, A. / Salavati, R. / Stuart, K.D. / Hol, W.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xdn.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xdn.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xdn_validation.pdf.gz | 771.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1xdn_full_validation.pdf.gz | 773.1 KB | Display | |
Data in XML | 1xdn_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1xdn_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/1xdn ftp://data.pdbj.org/pub/pdb/validation_reports/xd/1xdn | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31537.598 Da / Num. of mol.: 1 / Fragment: Adenylation domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: MP52 / Plasmid: pskB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GOLD DE3 / References: GenBank: 11067037, UniProt: P86927*PLUS |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.8 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, magnesium chloride, Tris, ATP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97885, 0.97899, 0.96112 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.1→50 Å / Num. obs: 95711 / % possible obs: 86.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 7.293 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 33.8 | ||||||||||||
Reflection shell | Highest resolution: 1.1 Å / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 33.8 / Num. unique all: 95711 / Rsym value: 0.064 / % possible all: 86.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.349 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.403 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20 /
|