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Yorodumi- PDB-6afk: Crystal structure of TrmD from Pseudomonas aeruginosa in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6afk | ||||||||||||
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Title | Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor | ||||||||||||
Components | tRNA (guanine-N(1)-)-methyltransferase | ||||||||||||
Keywords | TRANSFERASE / tRNA 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 | Pseudomonas aeruginosa UCBPP-PA14 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||||||||
Authors | Zhong, W. / Koay, A. / Wong, Y.W. / Sahili, A.E. / Nah, Q. / Kang, C. / Poulsen, A. / Chionh, Y.K. / McBee, M. / Matter, A. ...Zhong, W. / Koay, A. / Wong, Y.W. / Sahili, A.E. / Nah, Q. / Kang, C. / Poulsen, A. / Chionh, Y.K. / McBee, M. / Matter, A. / Hill, J. / Lescar, J. / Dedon, P.C. | ||||||||||||
Funding support | Singapore, 3items
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Citation | Journal: Acs Infect Dis. / Year: 2019 Title: Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N1G37) Methyltransferase (TrmD) Inhibitors. Authors: Zhong, W. / Koay, A. / Ngo, A. / Li, Y. / Nah, Q. / Wong, Y.H. / Chionh, Y.H. / Ng, H.Q. / Koh-Stenta, X. / Poulsen, A. / Foo, K. / McBee, M. / Choong, M.L. / El Sahili, A. / Kang, C. / ...Authors: Zhong, W. / Koay, A. / Ngo, A. / Li, Y. / Nah, Q. / Wong, Y.H. / Chionh, Y.H. / Ng, H.Q. / Koh-Stenta, X. / Poulsen, A. / Foo, K. / McBee, M. / Choong, M.L. / El Sahili, A. / Kang, C. / Matter, A. / Lescar, J. / Hill, J. / Dedon, P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6afk.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6afk.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 6afk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6afk_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6afk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6afk_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 6afk_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/6afk ftp://data.pdbj.org/pub/pdb/validation_reports/af/6afk | HTTPS FTP |
-Related structure data
Related structure data | 5wyqS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 3 - 250 / Label seq-ID: 22 - 269
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-Components
#1: Protein | Mass: 30336.164 Da / Num. of mol.: 2 / Fragment: UNP residues 5-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria) Strain: UCBPP-PA14 / Gene: trmD / Production host: Escherichia coli (E. coli) References: UniProt: Q02RL6, tRNA (guanine37-N1)-methyltransferase #2: Chemical | ChemComp-SAM / | #3: Chemical | ChemComp-9WO / | #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: 2.63 Å3/Da / Density % sol: 53.26 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-HCl at pH 8.6-8.8, 20%(v/v) MPD, 20%(w/v) PEG1000, 5%(w/v) PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→74.5 Å / Num. obs: 17233 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.75→2.88 Å / Rmerge(I) obs: 1.202 / Num. unique obs: 24835 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WYQ Resolution: 2.75→52.77 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.716 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 59.651 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→52.77 Å
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Refine LS restraints |
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