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- PDB-7rez: MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rez | |||||||||||||||
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Title | MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE | |||||||||||||||
![]() | tRNA (guanine-N(1)-)-methyltransferase | |||||||||||||||
![]() | TRANSFERASE / Methyltransferase / Mycobacterium Abscessus / S-Adenosyl-L-homocysteine | |||||||||||||||
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 | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 81.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rf0C ![]() 6nvrS S: Starting model for refinement C: citing same article ( |
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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: 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: 2.64 Å3/Da / Density % sol: 53.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein at 24mg/ml was incubated with 10mM SAH in DMSO in a 1 to 1 ratio; Buffer 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5. Drops were formed 1 to 1 ratio and crystals cryo ...Details: Protein at 24mg/ml was incubated with 10mM SAH in DMSO in a 1 to 1 ratio; Buffer 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5. Drops were formed 1 to 1 ratio and crystals cryo protected by adding 1 microliter of 50 percent Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→29.22 Å / Num. obs: 63130 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.4 Å2 / CC1/2: 1 / Net I/σ(I): 0.699 |
Reflection shell | Resolution: 1.64→1.681 Å / Num. unique obs: 4406 / CC1/2: 0.87 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6NVR Resolution: 1.64→29.21 Å / SU ML: 0.1913 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1937 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→29.21 Å
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Refine LS restraints |
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LS refinement shell |
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