[English] 日本語
Yorodumi- PDB-6joe: Crystal structure of TrmD from Pseudomonas aeruginosa in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6joe | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor | ||||||
Components | tRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase | ||||||
Keywords | TRANSFERASE / tRNA methyltransferase | ||||||
Function / homology | Function and homology information tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa UCBPP-PA14 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Zhong, W. / Pasunooti, K.K. / Balamkundu, S. / Wong, Y.W. / Nah, Q. / Liu, C.F. / Lescar, J. / Dedon, P.C. | ||||||
Funding support | Singapore, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6joe.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6joe.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 6joe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/6joe ftp://data.pdbj.org/pub/pdb/validation_reports/jo/6joe | HTTPS FTP |
---|
-Related structure data
Related structure data | 5zhiC 5zhjC 5zhkC 5zhlC 5zhmC 5zhnC 6jofC 5wyqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30336.164 Da / Num. of mol.: 2 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q02RL6, tRNA (guanine37-N1)-methyltransferase #2: Chemical | ChemComp-BWR / ~{ | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-SAM / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-HCl, pH 8.6-8.8, 20%(v/v) MPD, 20%(w/v) PEG 1000, and 5%(w/v) PEG200; the crystal was soaked with 1mM inhibitor. PH range: 8.6-8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→42.75 Å / Num. obs: 32130 / % possible obs: 99.8 % / Redundancy: 8.3 % / Biso Wilson estimate: 58.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.057 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.21→2.27 Å / Redundancy: 4 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 3 / Num. unique obs: 2724 / CC1/2: 0.874 / Rrim(I) all: 0.968 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WYQ Resolution: 2.21→42.75 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.242 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.193 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.44 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.21→42.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.21→2.23 Å / Total num. of bins used: 50
|