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- PDB-3mb5: Crystal structure of P. abyssi tRNA m1A58 methyltransferase in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mb5 | ||||||
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Title | Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-methionine | ||||||
![]() | SAM-dependent methyltransferase | ||||||
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Function / homology | ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guelorget, A. / Golinelli-Pimpaneau, B. | ||||||
![]() | ![]() Title: Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Authors: Guelorget, A. / Roovers, M. / Guerineau, V. / Barbey, C. / Li, X. / Golinelli-Pimpaneau, B. #1: Journal: Nucleic Acids Res. / Year: 2004 Title: A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase Authors: Roovers, M. / Wouters, J. / Bujnicki, J.M. / Tricot, C. / Stalon, V. / Grosjean, H. / Droogmans, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.7 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3lgaSC ![]() 3lhdC S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29162.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 352 molecules ![](data/chem/img/SAM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SAM / ![]() | ||||||
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#3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ChemComp-ACT / | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.33 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2.8M ammonium sulfate, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2010 / Details: bi-morph mirrors |
Radiation | Monochromator: cryogenically cooled monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→20 Å / Num. obs: 56562 / % possible obs: 99.8 % / Redundancy: 9.1 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.42 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5.1 / Num. unique all: 9295 / % possible all: 99.9 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB code 3LGA Resolution: 1.6→19.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.298 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.151 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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