[English] 日本語
Yorodumi- PDB-5hji: Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hji | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine | ||||||||||||
Components | tRNA (guanine(37)-N1)-methyltransferase Trm5a | ||||||||||||
Keywords | TRANSFERASE / Methyltransferase / Trm5a / SAM / Adenosine / tRNA modification | ||||||||||||
Function / homology | Function and homology information tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Xie, W. / Wang, C. / Jia, Q. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Crystal structures of the bifunctional tRNA methyltransferase Trm5a Authors: Wang, C. / Jia, Q. / Chen, R. / Wei, Y. / Li, J. / Ma, J. / Xie, W. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hji.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hji.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hji_validation.pdf.gz | 760.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5hji_full_validation.pdf.gz | 762 KB | Display | |
Data in XML | 5hji_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5hji_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/5hji ftp://data.pdbj.org/pub/pdb/validation_reports/hj/5hji | HTTPS FTP |
-Related structure data
Related structure data | 5hjjC 5hjkSC 5hjmC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40758.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Strain: GE5 / Orsay / Gene: trm5a, PYRAB01130, PAB2272 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) References: UniProt: Q9V2G1, tRNA (guanine37-N1)-methyltransferase |
---|---|
#2: Chemical | ChemComp-ADN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.1 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10-15% PEG3350, 100mM HEPES, pH7.5, 100mM Ca(OAc)2 and 100mM KCl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Nov 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→24.574 Å / Num. obs: 19382 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HJK Resolution: 2.2→24.574 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.72
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.574 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|