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- PDB-4e1b: Re-refinement of PDB entry 2EQA - SUA5 protein from Sulfolobus to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4e1b | ||||||
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Title | Re-refinement of PDB entry 2EQA - SUA5 protein from Sulfolobus tokodaii with bound threonylcarbamoyladenylate | ||||||
![]() | YrdC/Sua5 family protein | ||||||
![]() | RNA BINDING PROTEIN / YRDC/RIBB fold / YRDC domain / SUA5 domain / tRNA modification T6A | ||||||
Function / homology | ![]() L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA processing / regulation of translational fidelity / double-stranded RNA binding / tRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Parthier, C. / Goerlich, S. / Jaenecke, F. / Breithaupt, C. / Braeuer, U. / Fandrich, U. / Clausnitzer, D. / Wehmeier, U.F. / Boettcher, C. / Scheel, D. / Stubbs, M.T. | ||||||
![]() | ![]() Title: X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7. Authors: Agari, Y. / Sato, S. / Wakamatsu, T. / Bessho, Y. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / Shinkai, A. | ||||||
History |
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Remark 0 | THIS ENTRY 4E1B REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA OF R2EQASF ...THIS ENTRY 4E1B REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA OF R2EQASF DETERMINED BY THE AUTHORS OF THE PDB ENTRY 2EQA: Y.AGARI,A.SHINKAI,S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79 KB | Display | ![]() |
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PDB format | ![]() | 62.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 738 KB | Display | ![]() |
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Full document | ![]() | 740.5 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3venC ![]() 3veoC ![]() 3verC ![]() 3vesC ![]() 3vetC ![]() 3vewC ![]() 3vexC ![]() 3vezC ![]() 3vf2C ![]() 3vf4C C: citing same article ( |
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Similar 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: 39082.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-TXA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2EQA. |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.877 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.848 Å / Total num. of bins used: 20
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