[English] 日本語
Yorodumi- PDB-3g5r: Crystal structure of Thermus thermophilus TrmFO in complex with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g5r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Thermus thermophilus TrmFO in complex with tetrahydrofolate | ||||||
Components | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO | ||||||
Keywords | TRANSFERASE / tRNA methyltransferase FAD folate / FAD / Flavoprotein / Methyltransferase / tRNA processing | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate-tRNA-(uracil54-C5)-methyltransferase [NAD(P)H-oxidizing] / tRNA (uracil(54)-C5)-methyltransferase activity, 5,10-methylenetetrahydrofolate-dependent / tRNA wobble uridine modification / tRNA methylation / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Nishimasu, H. / Ishitani, R. / Hori, H. / Nureki, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase Authors: Nishimasu, H. / Ishitani, R. / Yamashita, K. / Iwashita, C. / Hirata, A. / Hori, H. / Nureki, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3g5r.cif.gz | 109 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3g5r.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 3g5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g5r_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3g5r_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3g5r_validation.xml.gz | 21 KB | Display | |
Data in CIF | 3g5r_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/3g5r ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g5r | HTTPS FTP |
-Related structure data
Related structure data | 3g5qC 3g5sSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48921.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: trmFO, TTHA1442 / Plasmid: pET-11 / Production host: Escherichia coli (E. coli) References: UniProt: Q5SID2, methylenetetrahydrofolate-tRNA-(uracil54-C5)-methyltransferase [NAD(P)H-oxidizing] |
---|
-Non-polymers , 5 types, 387 molecules
#2: Chemical | ChemComp-FAD / | ||
---|---|---|---|
#3: Chemical | ChemComp-THG / ( | ||
#4: Chemical | ChemComp-CA / | ||
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 20% PEG 8000, 0.2M calcium acetate, 0.1M Mes-NaOH (pH 6.5), 0.3mM tetrahydrofolic acid, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→35.85 Å / Num. obs: 60724 / Biso Wilson estimate: 16.68 Å2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G5S Resolution: 1.6→35.841 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.907 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 16.97 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.507 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.11 Å2 / Biso mean: 21.886 Å2 / Biso min: 8.57 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→35.841 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
|