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- PDB-3axz: Crystal structure of Haemophilus influenzae TrmD in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3axz | ||||||
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Title | Crystal structure of Haemophilus influenzae TrmD in complex with adenosine | ||||||
![]() | tRNA (guanine-N(1)-)-methyltransferase | ||||||
![]() | TRANSFERASE / trefoil knot / methyltransferase / AdoMet binding | ||||||
Function / homology | ![]() tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshida, K. / 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 | ![]() | 64.6 KB | Display | ![]() |
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PDB format | ![]() | 46.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ay0C ![]() 1uamS 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
#1: Protein | Mass: 29750.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ADN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M calcium acetate, 0.1M sodium cacodylate, 18% PEG 8000, pH 6.5, 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: 2.25→50 Å / Num. obs: 14775 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.152 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 668 / Rsym value: 0.427 / % possible all: 91.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UAM Resolution: 2.25→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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