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Yorodumi- PDB-6jki: Crystal structure and catalytic mechanism of the essential m1G37 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jki | ||||||
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Title | Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa | ||||||
Components | tRNA (guanine-N(1)-)-methyltransferase | ||||||
Keywords | TRANSFERASE / tRNA (guanine-N(1)-)-methyltransferase / TrmD / Pseudomonas aerugiona | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Jaroensuk, J. / Liew, C.W. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Zhong, W.H. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. ...Jaroensuk, J. / Liew, C.W. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Zhong, W.H. / McBee, M.E. / Thongdee, N. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M. | ||||||
Citation | Journal: Rna / Year: 2019 Title: Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa. Authors: Jaroensuk, J. / Wong, Y.H. / Zhong, W. / Liew, C.W. / Maenpuen, S. / Sahili, A.E. / Atichartpongkul, S. / Chionh, Y.H. / Nah, Q. / Thongdee, N. / McBee, M.E. / Prestwich, E.G. / DeMott, M.S. ...Authors: Jaroensuk, J. / Wong, Y.H. / Zhong, W. / Liew, C.W. / Maenpuen, S. / Sahili, A.E. / Atichartpongkul, S. / Chionh, Y.H. / Nah, Q. / Thongdee, N. / McBee, M.E. / Prestwich, E.G. / DeMott, M.S. / Chaiyen, P. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jki.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jki.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jki_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6jki_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6jki_validation.xml.gz | 22 KB | Display | |
Data in CIF | 6jki_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/6jki ftp://data.pdbj.org/pub/pdb/validation_reports/jk/6jki | HTTPS FTP |
-Related structure data
Related structure data | 5wyqC 5wyrC 5gm8S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28066.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: trmD, PA14_15990 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q02RL6, UniProt: Q9HXQ1*PLUS, tRNA (guanine37-N1)-methyltransferase |
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-Non-polymers , 6 types, 154 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.79 Å3/Da / Density % sol: 55.84 % / Description: Cubic shape |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 0.1M Tris-HCl, pH 8.4, 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 5% (w/v) PEG 200 PH range: 8.0 - 8.5 |
-Data collection
Diffraction | Mean temperature: 90 K / Ambient temp details: 90 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.890575 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2019 Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors |
Radiation | Monochromator: channel cut cryogenically cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.890575 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→49.19 Å / Num. obs: 37629 / % possible obs: 99.8 % / Redundancy: 19.6 % / Biso Wilson estimate: 93.27 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.192 / Net I/σ(I): 14.38 |
Reflection shell | Resolution: 2.59→2.73 Å / Num. unique obs: 6010 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GM8 Resolution: 2.59→24.73 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.571 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.62 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.294
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Displacement parameters | Biso mean: 72.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.59→24.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.61 Å / Total num. of bins used: 50
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