[English] 日本語
Yorodumi- PDB-4yvk: Crystal Structure of H. influenzae TrmD in complex with sinefungi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yvk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36C) | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/RNA / MTase / SPOUT / tRNA / TRANSFERASE-RNA complex | ||||||
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 | Haemophilus influenzae (bacteria) Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å | ||||||
Authors | Yoshida, K. / Ito, T. / Yokoyama, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. Authors: Ito, T. / Masuda, I. / Yoshida, K. / Goto-Ito, S. / Sekine, S. / Suh, S.W. / Hou, Y.M. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yvk.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yvk.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 4yvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/4yvk ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yvk | HTTPS FTP |
---|
-Related structure data
Related structure data | 4yvgC 4yvhC 4yviSC 4yvjC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29750.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria) Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trmD, HI_0202 / Production host: Escherichia coli (E. coli) References: UniProt: P43912, tRNA (guanine37-N1)-methyltransferase #2: RNA chain | | Mass: 23818.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 12057205 #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: sodium acetate trihydrate, ammonium phosphate monobasic, PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 18509 / % possible obs: 99.8 % / Redundancy: 7.3 % / Net I/σ(I): 20.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YVI Resolution: 3.002→43.725 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.58 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.418 Å2 / ksol: 0.299 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.002→43.725 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|