+Open data
-Basic information
Entry | Database: PDB / ID: 4k25 | ||||||
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Title | Crystal Structure of yeast Qri7 homodimer | ||||||
Components | Probable tRNA threonylcarbamoyladenosine biosynthesis protein QRI7, mitochondrial | ||||||
Keywords | BIOSYNTHETIC PROTEIN / ASKHA-fold / N6-threonylcarbamoylation enzyme / RNA and metabolite binding / mitochondria | ||||||
Function / homology | Function and homology information mitochondrial tRNA threonylcarbamoyladenosine modification / N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / nucleotidase activity / tRNA threonylcarbamoyladenosine modification / tRNA binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Neculai, D. / Wan, L. / Mao, D.Y. / Sicheri, F. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Authors: Wan, L.C. / Mao, D.Y. / Neculai, D. / Strecker, J. / Chiovitti, D. / Kurinov, I. / Poda, G. / Thevakumaran, N. / Yuan, F. / Szilard, R.K. / Lissina, E. / Nislow, C. / Caudy, A.A. / Durocher, D. / Sicheri, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k25.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k25.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 4k25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k25 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k25 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two-fold axis: -X, -Y, Z + (1 0 0) |
-Components
#1: Protein | Mass: 42989.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: QRI7, YDL104C, D2366 / Production host: Escherichia coli (E. coli) / References: UniProt: P43122 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.77 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris, 8% PEG8000, 0.2M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2011 |
Radiation | Monochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→20.58 Å / Num. all: 17164 / Num. obs: 9434 / % possible obs: 55 % / Observed criterion σ(F): 2.54 / Observed criterion σ(I): 2.54 / Biso Wilson estimate: 77.86 Å2 |
Reflection shell | Resolution: 2.88→2.98 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→20.58 Å / Cor.coef. Fo:Fc: 0.9059 / Cor.coef. Fo:Fc free: 0.8745 / Cross valid method: THROUGHOUT / σ(F): 3.3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 81.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.625 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→20.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.24 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 46.0749 Å / Origin y: 17.508 Å / Origin z: 24.6981 Å
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Refinement TLS group | Selection details: { A|33 - A|602 } |