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- PDB-3ay0: Crystal structure of Methanocaldococcus jannaschii Trm5 in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ay0 | ||||||
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Title | Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine | ||||||
![]() | Uncharacterized protein MJ0883 | ||||||
![]() | TRANSFERASE / Rossmann Fold / methyltransferase / AdoMet binding | ||||||
Function / homology | ![]() tRNA methyltransferase activity / tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goto-Ito, S. / Ito, T. / Hou, Y.M. / Yokoyama, S. | ||||||
![]() | ![]() Title: Differentiating analogous tRNA methyltransferases by fragments of the methyl donor. Authors: Lahoud, G. / Goto-Ito, S. / Yoshida, K. / Ito, T. / Yokoyama, S. / Hou, Y.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 | ![]() | 140.1 KB | Display | ![]() |
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PDB format | ![]() | 109.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.8 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3axzC ![]() 2yx1S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39071.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MJ0883, Trm5 / Plasmid: pET-26b / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.02M HEPES, 0.175M sodium thiocyanate, 8% PEG 3350, 5% PEGMME 550, 0.002M zinc sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 14439 / % possible obs: 99.8 % / Observed criterion σ(I): -2 / Redundancy: 3.7 % / Biso Wilson estimate: 86.7 Å2 / Rsym value: 0.109 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 3.05→3.1 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 706 / Rsym value: 0.468 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YX1 Resolution: 3.05→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.05→50 Å
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Refine LS restraints |
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