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Yorodumi- PDB-1wju: Solution structure of N-terminal ubiquitin-like domain of human N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wju | ||||||
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Title | Solution structure of N-terminal ubiquitin-like domain of human NEDD8 ultimate buster-1 | ||||||
Components | NEDD8 ultimate buster-1 | ||||||
Keywords | PROTEIN BINDING / Ubiquitin-like domain / NEDD8 ultimate buster-1 / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of ubiquitin-dependent protein catabolic process / response to type II interferon / response to tumor necrosis factor / post-translational protein modification / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleolus / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Yoneyama, M. / Koshiba, S. / Tochio, N. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of N-terminal ubiquitin-like domain of human NEDD8 ultimate buster-1 Authors: Yoneyama, M. / Koshiba, S. / Tochio, N. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wju.cif.gz | 611.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wju.ent.gz | 528.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/1wju ftp://data.pdbj.org/pub/pdb/validation_reports/wj/1wju | HTTPS FTP |
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-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: 11038.656 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: IMS cDNA SYN05355 / Plasmid: P040301-74 / References: UniProt: Q9Y5A7 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1mM Ubiquitin-like domain U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |