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- PDB-3lga: 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: 3lga | ||||||
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Title | Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine | ||||||
![]() | 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 | ![]() | 220.6 KB | Display | ![]() |
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PDB format | ![]() | 177.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3lhdSC ![]() 3mb5C 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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Unit cell |
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Components
#1: Protein | Mass: 28920.662 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SAH / ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2.4M ammonium sulfate, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2009 / 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: 2.05→34.86 Å / Num. obs: 162057 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.54 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.1 / Num. unique all: 23768 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3LHD Resolution: 2.05→34.86 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.7 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.108 / 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: 38.427 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→34.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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