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Yorodumi- PDB-4e1b: Re-refinement of PDB entry 2EQA - SUA5 protein from Sulfolobus to... -
+Open data
-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 | ||||||
Components | YrdC/Sua5 family protein | ||||||
Keywords | RNA BINDING PROTEIN / YRDC/RIBB fold / YRDC domain / SUA5 domain / tRNA modification T6A | ||||||
Function / homology | Function and homology information 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 | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 1.8 Å | ||||||
Authors | Parthier, C. / Goerlich, S. / Jaenecke, F. / Breithaupt, C. / Braeuer, U. / Fandrich, U. / Clausnitzer, D. / Wehmeier, U.F. / Boettcher, C. / Scheel, D. / Stubbs, M.T. | ||||||
Citation | Journal: Proteins / Year: 2008 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) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e1b.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e1b.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 4e1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e1b_validation.pdf.gz | 738 KB | Display | wwPDB validaton report |
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Full document | 4e1b_full_validation.pdf.gz | 740.5 KB | Display | |
Data in XML | 4e1b_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4e1b_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/4e1b ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e1b | HTTPS FTP |
-Related structure data
Related structure data | 3venC 3veoC 3verC 3vesC 3vetC 3vewC 3vexC 3vezC 3vf2C 3vf4C 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: 39082.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: STK_15260, SUA5 / Plasmid: pET-21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL-X / References: UniProt: Q970S6 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-TXA / |
#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: 2.23 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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→34.87 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.24 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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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