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Yorodumi- PDB-6ia6: Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ia6 | |||||||||
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Title | Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA | |||||||||
Components | ELP3 family, ELP3 family | |||||||||
Keywords | TRANSFERASE / tRNA binding / Elongator complex / non-canonical acetyltransferase / acetyl-CoA hydrolysis | |||||||||
Function / homology | Function and homology information tRNA uridine(34) acetyltransferase activity / tRNA acetylation / tRNA wobble uridine modification / S-adenosyl-L-methionine binding / iron-sulfur cluster binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 4 iron, 4 sulfur cluster binding / tRNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Dehalococcoides mccartyi BTF08 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Lin, T.Y. / Glatt, S. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Authors: Lin, T.Y. / Abbassi, N.E.H. / Zakrzewski, K. / Chramiec-Glabik, A. / Jemiola-Rzeminska, M. / Rozycki, J. / Glatt, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ia6.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ia6.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ia6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/6ia6 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/6ia6 | HTTPS FTP |
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-Related structure data
Related structure data | 6ia8C 6iadC 6iazC 5l7lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49940.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Dehalococcoides mccartyi Elp3 and desulfo-CoA Source: (gene. exp.) Dehalococcoides mccartyi BTF08 (bacteria) Gene: btf_573 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A1C7D1B7 |
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#2: Chemical | ChemComp-DCA / |
#3: Chemical | ChemComp-FES / |
#4: Chemical | ChemComp-PO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH 6.3 and 4% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 15372 / % possible obs: 99 % / Redundancy: 4.4 % / Rrim(I) all: 0.141 / Net I/σ(I): 9.75 |
Reflection shell | Resolution: 2.7→2.77 Å / Rrim(I) all: 2.099 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L7L Resolution: 2.7→43.305 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→43.305 Å
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Refine LS restraints |
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LS refinement shell |
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