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- PDB-7rf0: MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rf0 | |||||||||||||||
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Title | MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND MAGNESIUM | |||||||||||||||
![]() | tRNA (guanine-N(1)-)-methyltransferase | |||||||||||||||
![]() | TRANSFERASE / METHYLTRANSFERASE / MYCOBACTERIUM ABSCESSUS | |||||||||||||||
Function / homology | ![]() tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / metal ion binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Prucha, G.R. / Ismail, M. / Suske, A. / Das, B. / Oz, M. / Perez, A. / Bolen, R. / Jayaraman, S. / Stojanoff, V. / Halloran, J. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of divalent Mg+2 dependent Mycobacterium abscessus tRNA (m1 G37) Methyltransferase (TrmD) Authors: Prucha, G.R. / Ismail, M. / Suske, A. / Perez, A. / Bolen, R. / Jayaraman, S. / Stojanoff, V. / Halloran, J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.7 KB | Display | ![]() |
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PDB format | ![]() | 79.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rezC ![]() 6nvrS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 25465.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: trmD, SAMEA2161603_03547, SAMEA2275821_02238, SAMEA2275847_06627 Production host: ![]() ![]() References: UniProt: A0A1M9INC4, tRNA (guanine37-N1)-methyltransferase #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Drops were 2ul of protein 24 mg/ml and 2ul buffer (0.1M sodium cacodylate and 2M ammonium nitrate pH 6.5); co-crystallized with SAH in a 1:1 ratio at a final concentration of 5mM SAH in the ...Details: Drops were 2ul of protein 24 mg/ml and 2ul buffer (0.1M sodium cacodylate and 2M ammonium nitrate pH 6.5); co-crystallized with SAH in a 1:1 ratio at a final concentration of 5mM SAH in the drops; and 4ul MgSO4 at 10mM were added to the drops before cryo-cooling |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 2, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9802 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→28.24 Å / Num. obs: 68820 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.77 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.56→1.6 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4995 / CC1/2: 0.781 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6NVR Resolution: 1.59→28.22 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→28.22 Å
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Refine LS restraints |
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LS refinement shell |
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