+Open data
-Basic information
Entry | Database: PDB / ID: 1vej | ||||||
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Title | Solution Structure of RSGI RUH-016, a UBA Domain from mouse cDNA | ||||||
Components | RIKEN cDNA 4931431F19 | ||||||
Keywords | structural genomics / unknown function / UBA domain / three helix bundle / ubiquitin associated domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information polyubiquitin modification-dependent protein binding / ubiquitin-dependent protein catabolic process / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Higuchi, Y. / Abe, T. / Hirota, H. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of RSGI RUH-016, a UBA Domain from mouse cDNA Authors: Higuchi, Y. / Abe, T. / Hirota, H. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vej.cif.gz | 402.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vej.ent.gz | 336.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vej_validation.pdf.gz | 341.5 KB | Display | wwPDB validaton report |
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Full document | 1vej_full_validation.pdf.gz | 470.9 KB | Display | |
Data in XML | 1vej_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 1vej_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1vej ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1vej | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7504.151 Da / Num. of mol.: 1 / Fragment: UBA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis system Gene: Mus musculus RIKEN cDNA 4931431F19 gene (4931431F19Rik), mRNA Plasmid: P030324-24 / References: UniProt: Q9D4I8 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1.17mM UBA domain U-15N, 13C; 20mM PiNa; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |