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- PDB-4yqb: Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yqb | ||||||
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Title | Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds | ||||||
![]() | tRNA (guanine-N(1)-)-methyltransferase | ||||||
![]() | transferase/transferase inhibitor / TrmD / SAM-binding / knot / transferase-transferase inhibitor complex | ||||||
Function / homology | ![]() tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elkins, P.A. / Bonnette, W.G. / Stuckey, J.A. | ||||||
![]() | ![]() Title: Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds Authors: Elkins, P.A. / Bonnette, W.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.6 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ypwC ![]() 4ypxC ![]() 4ypyC ![]() 4ypzC ![]() 4yq0C ![]() 4yq2C ![]() 4yq3C ![]() 4yq4C ![]() 4yq5C ![]() 4yq6C ![]() 4yq7C ![]() 4yq8C ![]() 4yq9C ![]() 4yqaC ![]() 4yqcC ![]() 4yqdC ![]() 4yqgC ![]() 4yqiC ![]() 4yqjC ![]() 4yqkC ![]() 4yqlC ![]() 4yqnC ![]() 4yqoC ![]() 4yqpC ![]() 4yqqC ![]() 4yqrC ![]() 4yqsC ![]() 4yqtC ![]() 5d9fC ![]() 1p9pS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 28384.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trmD, HI_0202 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: P43912, tRNA (guanine37-N1)-methyltransferase |
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#2: Chemical | ChemComp-4GM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution:( 12/mg/mL in 100mM HEPES pH 7.5, 150mM NaCl, 10mM MgCl2 2mM DTT) Well solution: (20% PEG3,350 and 0.2M potassium citrate tribasic monohydrate). 4uL of S-adenosyl methionine ...Details: Protein solution:( 12/mg/mL in 100mM HEPES pH 7.5, 150mM NaCl, 10mM MgCl2 2mM DTT) Well solution: (20% PEG3,350 and 0.2M potassium citrate tribasic monohydrate). 4uL of S-adenosyl methionine in water were added to 100uL of protein and allowed to incubate on ice for 1 hour before protein was mixed with well at 1:1 ratio.Seeding used to improve crystals. Compound stock solutions (either 100mM or 1M stocks) were added up to a final drop concentration of 4.8% DMSO. Crystals were soaked for 4-6 hours. 20% glycerol in well solution was used as cryoprotectant for a quick dip of crystal in liquid N2. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 27, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→30 Å / Num. obs: 22781 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.08 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.063 / Net I/av σ(I): 28.867 / Net I/σ(I): 10.7 / Num. measured all: 148731 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P9P Resolution: 2.1→29.261 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.77 Å2 / Biso mean: 37.9863 Å2 / Biso min: 16.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→29.261 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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