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Yorodumi- PDB-6ia8: Apo crystal structure of archaeal Methanocaldococcus infernus Elp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ia8 | |||||||||
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Title | Apo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-19) | |||||||||
Components | Histone acetyltransferase, 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 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 4 iron, 4 sulfur cluster binding / tRNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Methanocaldococcus infernus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 6ia8.cif.gz | 265.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ia8.ent.gz | 216.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ia8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/6ia8 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/6ia8 | HTTPS FTP |
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-Related structure data
Related structure data | 6ia6C 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
#1: Protein | Mass: 59876.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: apo structure of Methanocaldococcus infernus Elp3 (del1-19) Source: (gene. exp.) Methanocaldococcus infernus (archaea) / Gene: Metin_0452 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: D5VRB9, histone acetyltransferase | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M phosphate/citrate (pH 3.8), 0.2 M LiSO4 and 12% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 41022 / % possible obs: 98.3 % / Redundancy: 24.1 % / Rrim(I) all: 0.068 / Net I/σ(I): 33.38 |
Reflection shell | Resolution: 1.9→1.95 Å / Rrim(I) all: 1.582 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L7L Resolution: 1.9→44.859 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.859 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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