[English] 日本語
Yorodumi- PDB-5gm8: Methylation at position 32 of tRNA catalyzed by TrmJ alters oxida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gm8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa | |||||||||
Components | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | |||||||||
Keywords | TRANSFERASE / Pseudomonas aeruginosa / tRNA methyltransferase / TrmJ / oxidative stress / tRNA modification / wobble base | |||||||||
Function / homology | Function and homology information tRNA (cytidine32/uridine32-2'-O)-methyltransferase / tRNA nucleoside ribose methylation / : / RNA binding / cytosol Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Jaroensuk, J. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Liew, C.W. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. ...Jaroensuk, J. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Liew, C.W. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M. | |||||||||
Funding support | Singapore, 1items
| |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa. Authors: Jaroensuk, J. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Liew, C.W. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5gm8.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5gm8.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 5gm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gm8_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5gm8_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5gm8_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 5gm8_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/5gm8 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gm8 | HTTPS FTP |
-Related structure data
Related structure data | 5gmbC 5gmcC 4cndS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18790.424 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: B136-33 / Gene: trmJ / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A072ZPM2, tRNA (cytidine32/uridine32-2'-O)-methyltransferase #2: Chemical | ChemComp-SFG / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.89 % / Description: Solid hexagonal crystal |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate, Tris, Lithium sulfate / Temp details: 293.15 |
-Data collection
Diffraction | Mean temperature: 110 K / Ambient temp details: 110 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2014 / Details: toroidal focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20.72 Å / Num. obs: 34918 / % possible obs: 95.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.95 Å2 / Rmerge(I) obs: 0.099 / Net I/av σ(I): 1.9 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.24→2.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.9 / % possible all: 95.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CND Resolution: 2.2→20.72 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.28 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.198
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.57 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→20.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
|