+Open data
-Basic information
Entry | Database: PDB / ID: 6nbj | ||||||
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Title | Qri7 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / DIMER | ||||||
Function / homology | Function and homology information mitochondrial tRNA threonylcarbamoyladenosine modification / N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.94 Å | ||||||
Authors | Stec, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP. Authors: Tominaga, T. / Kobayashi, K. / Ishii, R. / Ishitani, R. / Nureki, O. | ||||||
History |
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Remark 0 | THIS ENTRY 6NBJ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3WUH, DETERMINED BY T. ...THIS ENTRY 6NBJ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3WUH, DETERMINED BY T.TOMINAGA,K.KOBAYASHI,R.ISHII,R.ISHITANI,O.NUREKI |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nbj.cif.gz | 167.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nbj.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nbj_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6nbj_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6nbj_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 6nbj_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/6nbj ftp://data.pdbj.org/pub/pdb/validation_reports/nb/6nbj | HTTPS FTP |
-Related structure data
Related structure data | 6nakC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 3 molecules ABC
#1: Protein | Mass: 42585.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: QRI7, YDL104C, D2366 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P43122, N6-L-threonylcarbamoyladenine synthase #2: RNA chain | | Mass: 1175.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast) |
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-Non-polymers , 7 types, 32 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-ATP / | #7: Chemical | ChemComp-SO4 / | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 400, 3% w/v dextran sulfate sodium salt (Mr 5000), 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→50.1 Å / Num. obs: 22014 / % possible obs: 99.8 % / Redundancy: 4.8 % / Rmerge F all: 0.089 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.94→3.07 Å |
-Processing
Software |
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Refinement | Resolution: 2.94→50.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.988 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.96 Å2
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Refinement step | Cycle: 1 / Resolution: 2.94→50.06 Å
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Refine LS restraints |
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