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- PDB-6qrb: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qrb | ||||||
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Title | Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor | ||||||
![]() | tRNA (guanine-N(1)-)-methyltransferase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Thomas, S.E. / Whitehouse, A.J. / Coyne, A.G. / Abell, C. / Mendes, V. / Blundell, T.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Development of Inhibitors against Mycobacterium abscessus tRNA (m 1 G37) Methyltransferase (TrmD) Using Fragment-Based Approaches. Authors: Whitehouse, A.J. / Thomas, S.E. / Brown, K.P. / Fanourakis, A. / Chan, D.S. / Libardo, M.D.J. / Mendes, V. / Boshoff, H.I.M. / Floto, R.A. / Abell, C. / Blundell, T.L. / Coyne, A.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 | ![]() | 102.5 KB | Display | ![]() |
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PDB format | ![]() | 76.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qqqC ![]() 6qqrC ![]() 6qqtC ![]() 6qquC ![]() 6qqvC ![]() 6qqwC ![]() 6qqzC ![]() 6qr0C ![]() 6qr1C ![]() 6qr2C ![]() 6qr3C ![]() 6qr4C ![]() 6qr7C ![]() 6qr9C ![]() 6qraC ![]() 6qrcC ![]() 6qrdC ![]() 6qreC ![]() 6qrfC ![]() 6qrgC ![]() 6nvrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 26434.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: B1MDI3, ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.08M Sodium cacodylate pH 6.5 -7.0, 1-2 M Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||
Reflection | Resolution: 1.66→57.91 Å / Num. obs: 60366 / % possible obs: 98.2 % / Redundancy: 8.3 % / Biso Wilson estimate: 25.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.044 / Rrim(I) all: 0.127 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Phasing MR | Packing: 0 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6NVR Resolution: 1.66→43.39 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.32 Å2 / Biso mean: 31.0783 Å2 / Biso min: 17.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.66→43.39 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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