+Open data
-Basic information
Entry | Database: PDB / ID: 5l7j | ||||||
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Title | Crystal Structure of Elp3 from Dehalococcoides mccartyi | ||||||
Components | ELP3 family | ||||||
Keywords | TRANSLATION / Elongator / tRNA modification / Elp3 | ||||||
Function / homology | Function and homology information tRNA carboxymethyluridine synthase / acyltransferase activity / 2 iron, 2 sulfur cluster binding / tRNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Dehalococcoides mccartyi BTF08 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Glatt, S. / Mueller, C.W. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2016 Title: Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi. Authors: Glatt, S. / Zabel, R. / Kolaj-Robin, O. / Onuma, O.F. / Baudin, F. / Graziadei, A. / Taverniti, V. / Lin, T.Y. / Baymann, F. / Seraphin, B. / Breunig, K.D. / Muller, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l7j.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l7j.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 5l7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l7j_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 5l7j_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 5l7j_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5l7j_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/5l7j ftp://data.pdbj.org/pub/pdb/validation_reports/l7/5l7j | HTTPS FTP |
-Related 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: 51772.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dehalococcoides mccartyi BTF08 (bacteria) Gene: btf_573 / Production host: Escherichia coli (E. coli) / References: UniProt: M1Q3U6, UniProt: A0A1C7D1B6*PLUS |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-FES / |
#4: 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: 2.73 Å3/Da / Density % sol: 54.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 6.3 and 4% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97923 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 58785 / % possible obs: 99.5 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 10.6 % / Rmerge(I) obs: 2.309 / Mean I/σ(I) obs: 1.03 / CC1/2: 0.567 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→43.294 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→43.294 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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