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Yorodumi- PDB-6qqq: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qqq | ||||||
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Title | Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor | ||||||
Components | tRNA (guanine-N(1)-)-methyltransferase | ||||||
Keywords | TRANSFERASE / TrmD / tRNA methyltransferase / SPOUT methyltransferase | ||||||
Function / homology | Function and homology information tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium abscessus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Thomas, S.E. / Whitehouse, A.J. / Coyne, A.G. / Abell, C. / Mendes, V. / Blundell, T.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Development of Inhibitors againstMycobacterium abscessustRNA (m1G37) 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qqq.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qqq.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 6qqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qqq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6qqq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6qqq_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 6qqq_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/6qqq ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qqq | HTTPS FTP |
-Related structure data
Related structure data | 6qqrC 6qqtC 6qquC 6qqvC 6qqwC 6qqzC 6qr0C 6qr1C 6qr2C 6qr3C 6qr4C 6qr7C 6qr9C 6qraC 6qrbC 6qrcC 6qrdC 6qreC 6qrfC 6qrgC 6nvrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium abscessus (bacteria) / Gene: trmD, MAB_3226c / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å | ||||||||||||||||||||||||
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: 1.85→77.66 Å / Num. obs: 42344 / % possible obs: 97.3 % / Redundancy: 9.4 % / Biso Wilson estimate: 33.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Rrim(I) all: 0.096 / Net I/σ(I): 13.6 / Num. measured all: 397011 / Scaling rejects: 2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Packing: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NVR Resolution: 1.85→57.638 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.78 Å2 / Biso mean: 38.6286 Å2 / Biso min: 21.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→57.638 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: 15
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