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Yorodumi- PDB-4rdh: Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rdh | ||||||
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Title | Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA | ||||||
Components | tRNA threonylcarbamoyladenosine dehydratase | ||||||
Keywords | LIGASE / Rossman fold / dehydratase | ||||||
Function / homology | Function and homology information Ligases; Forming carbon-oxygen bonds / tRNA threonylcarbamoyladenosine dehydratase / cyclic threonylcarbamoyladenosine biosynthetic process / ubiquitin-like modifier activating enzyme activity / sodium ion binding / potassium ion binding / protein homodimerization activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Park, S.Y. / Kim, S. / Lee, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity. Authors: Kim, S. / Lee, H. / Park, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rdh.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rdh.ent.gz | 167.4 KB | Display | PDB format |
PDBx/mmJSON format | 4rdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/4rdh ftp://data.pdbj.org/pub/pdb/validation_reports/rd/4rdh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31236.322 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tcdA, ygdL, csdL / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q46927, Ligases; Forming carbon-oxygen bonds #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #5: 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 Å3/Da / Density % sol: 38.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% (w/v) PEG 3350, 0.1 M Hepes, pH 7.5 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97902 Å |
Detector | Type: ADSC QUANTUM 270r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97902 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 57374 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 5.38 / Rsym value: 0.375 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.327 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.155 Å / Total num. of bins used: 20
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