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- PDB-6qr8: 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: 6qr8 | ||||||
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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 | ||||||
![]() | TRANSFERASE / TrmD / tRNA methyltransferase / SPOUT methyltransferase | ||||||
Function / homology | ![]() tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol 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: Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification. Authors: Thomas, S.E. / Whitehouse, A.J. / Brown, K. / Burbaud, S. / Belardinelli, J.M. / Sangen, J. / Lahiri, R. / Libardo, M.D.J. / Gupta, P. / Malhotra, S. / Boshoff, H.I.M. / Jackson, M. / Abell, ...Authors: Thomas, S.E. / Whitehouse, A.J. / Brown, K. / Burbaud, S. / Belardinelli, J.M. / Sangen, J. / Lahiri, R. / Libardo, M.D.J. / Gupta, P. / Malhotra, S. / Boshoff, H.I.M. / Jackson, M. / Abell, C. / Coyne, A.G. / Blundell, T.L. / Floto, R.A. / Mendes, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.2 KB | Display | ![]() |
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PDB format | ![]() | 72.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6nvrSC ![]() 6nw6C ![]() 6nw7C ![]() 6qo2C ![]() 6qo3C ![]() 6qo4C ![]() 6qo6C ![]() 6qoaC ![]() 6qocC ![]() 6qodC ![]() 6qoeC ![]() 6qofC ![]() 6qogC ![]() 6qohC ![]() 6qoiC ![]() 6qojC ![]() 6qokC ![]() 6qolC ![]() 6qomC ![]() 6qonC ![]() 6qooC ![]() 6qopC ![]() 6qoqC ![]() 6qorC ![]() 6qosC ![]() 6qotC ![]() 6qouC ![]() 6qovC ![]() 6qowC ![]() 6qoxC ![]() 6qqsC ![]() 6qqxC ![]() 6qqyC ![]() 6qr5C ![]() 6qr6C 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, tRNA (guanine37-N1)-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.29 % |
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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: 0.9686 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.15→76.33 Å / Num. obs: 27662 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 40.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.046 / Rrim(I) all: 0.142 / Net I/σ(I): 10.6 / Num. measured all: 260273 / Scaling rejects: 1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Phasing MR | Packing: 1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6NVR Resolution: 2.15→57.198 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.15 Å2 / Biso mean: 44.3044 Å2 / Biso min: 23.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→57.198 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: 10 / % reflection obs: 100 %
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