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- PDB-6qqx: 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: 6qqx | ||||||
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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 | ![]() | 94.8 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 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 ![]() 6qqyC ![]() 6qr5C ![]() 6qr6C ![]() 6qr8C 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: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.46 % |
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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 PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.69→78.22 Å / Num. obs: 14581 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.985 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.087 / Rrim(I) all: 0.257 / Net I/σ(I): 8.3 / Num. measured all: 125661 / Scaling rejects: 3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6NVR Resolution: 2.69→58.01 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.869 / SU B: 14.084 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.319 / ESU R Free: 0.361 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.52 Å2 / Biso mean: 35.875 Å2 / Biso min: 10.07 Å2
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Refinement step | Cycle: final / Resolution: 2.69→58.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.693→2.763 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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