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- PDB-5gmb: Methylation at position 32 of tRNA catalyzed by TrmJ alters oxida... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gmb | ||||||
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Title | Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa | ||||||
![]() | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | ||||||
![]() | TRANSFERASE / Pseudomonas aeruginosa / tRNA methyltransferase / TrmJ / oxidative stress / tRNA modification / wobble base | ||||||
Function / homology | ![]() tRNA (cytidine32/uridine32-2'-O)-methyltransferase / tRNA nucleoside ribose methylation / tRNA (uracil-2'-O-)-methyltransferase activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51 KB | Display | ![]() |
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PDB format | ![]() | 35.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.5 KB | Display | ![]() |
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Full document | ![]() | 431.5 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gm8C ![]() 5gmcC ![]() 4cndS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18514.092 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A072ZPM2, tRNA (cytidine32/uridine32-2'-O)-methyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.97 % / Description: solid cubic crystals |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MgCl2, CaCl2, PEG MME 550, PEG 20000, MOPS/Na-HEPES pH7.5 Temp details: 293.15 |
-Data collection
Diffraction | Mean temperature: 110 K / Ambient temp details: 110 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2015 / 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: 1.62→30.03 Å / Num. obs: 29132 / % possible obs: 95.4 % / Redundancy: 9.9 % / Biso Wilson estimate: 18.25 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.9 / % possible all: 71.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CND Resolution: 1.62→29.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.084 / SU Rfree Blow DPI: 0.083 / SU Rfree Cruickshank DPI: 0.078
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Displacement parameters | Biso mean: 20.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→29.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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