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Open data
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Basic information
Entry | Database: PDB / ID: 4yed | ||||||
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Title | TcdA (CsdL) | ||||||
![]() | tRNA threonylcarbamoyladenosine dehydratase | ||||||
![]() | LIGASE / N6-threonylcarbamoyladenosine dehydratase tRNA modification | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kim, S. / Park, S.Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.1 KB | Display | ![]() |
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PDB format | ![]() | 175.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 45.4 KB | Display | |
Data in CIF | ![]() | 64.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29300.357 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q46927, Ligases; Forming carbon-oxygen bonds #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) PEG 3350 and 0.15 M DL-malic acid, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 76402 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 26.6 |
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Processing
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Refinement | Resolution: 1.9→32.766 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.248 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.13 / 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: 30.049 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.766 Å
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