[English] 日本語
Yorodumi- PDB-5eqj: Crystal structure of the two-subunit tRNA m1A58 methyltransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eqj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the two-subunit tRNA m1A58 methyltransferase from Saccharomyces cerevisiae | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / tRNA / complex / methyltransferase | ||||||
Function / homology | Function and homology information tRNA (adenine58-N1)-methyltransferase / : / tRNA (m1A) methyltransferase complex / tRNA methylation / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Zhu, Y. / Wang, M. / Wang, C. / Fan, X. / Jiang, X. / Teng, M. / Li, X. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Crystal structure of the two-subunit tRNA m(1)A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae. Authors: Wang, M. / Zhu, Y. / Wang, C. / Fan, X. / Jiang, X. / Ebrahimi, M. / Qiao, Z. / Niu, L. / Teng, M. / Li, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5eqj.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5eqj.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 5eqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eqj_validation.pdf.gz | 429.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5eqj_full_validation.pdf.gz | 431.6 KB | Display | |
Data in XML | 5eqj_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 5eqj_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/5eqj ftp://data.pdbj.org/pub/pdb/validation_reports/eq/5eqj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 55720.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: GCD10, TIF33, TRM6, YNL062C, N2422 / Production host: Escherichia coli (E. coli) / References: UniProt: P41814 |
---|---|
#2: Protein | Mass: 43987.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: GCD14, TRM61, YJL125C, J0710 / Production host: Escherichia coli (E. coli) References: UniProt: P46959, tRNA (adenine58-N1)-methyltransferase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.97 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M KCl, 0.1 M Tris HCl pH 8.5, 15% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 57936 / % possible obs: 99.8 % / Redundancy: 8.3 % / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3.4 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.2→39.029 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.93 / 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: 2.2→39.029 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|