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- PDB-5zhk: Crystal structure of TrmD from Mycobacterium tuberculosis in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zhk | ||||||
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Title | Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor | ||||||
![]() | tRNA (guanine-N(1)-)-methyltransferase | ||||||
![]() | TRANSFERASE / tRNA methyltransferase | ||||||
Function / homology | ![]() tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.W. / Nah, Q. / Liu, C.F. / Lescar, J. / Dedon, P.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism. Authors: Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.H. / Nah, Q. / Gadi, V. / Gnanakalai, S. / Chionh, Y.H. / McBee, M.E. / Gopal, P. / Lim, S.H. / Olivier, N. / Buurman, E.T. / Dick, T. ...Authors: Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.H. / Nah, Q. / Gadi, V. / Gnanakalai, S. / Chionh, Y.H. / McBee, M.E. / Gopal, P. / Lim, S.H. / Olivier, N. / Buurman, E.T. / Dick, T. / Liu, C.F. / Lescar, J. / Dedon, P.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.8 KB | Display | ![]() |
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PDB format | ![]() | 41.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 721.4 KB | Display | ![]() |
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Full document | ![]() | 722.3 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zhiC ![]() 5zhjC ![]() 5zhlC ![]() 5zhmC ![]() 5zhnC ![]() 6joeC ![]() 6jofC ![]() 5wyqS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26170.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H37Rv / Gene: trmD / Production host: ![]() ![]() References: UniProt: P9WFY7, tRNA (guanine37-N1)-methyltransferase |
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#2: Chemical | ChemComp-9D6 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM Bis-Tris at pH 6.5, 20%(w/v) PEG3350, 0.1M ammonium acetate; the crystal was soaked with 1 mM inhibitor. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→58.08 Å / Num. obs: 8972 / % possible obs: 94.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Rmerge(I) obs: 0.438 / Num. unique obs: 3432 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WYQ Resolution: 2.3→58.08 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.449 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.237
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Displacement parameters | Biso mean: 28.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→58.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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