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Yorodumi- PDB-1wji: Solution Structure of the UBA Domain of Human Tudor Domain Contai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wji | ||||||
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Title | Solution Structure of the UBA Domain of Human Tudor Domain Containing Protein 3 | ||||||
Components | Tudor domain containing protein 3 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / UBA domain / tudor domain containing 3 / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information DNA topoisomerase III-beta-TDRD3 complex / DNA topological change / methylated histone binding / chromatin organization / transcription coactivator activity / chromatin binding / Golgi apparatus / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Kamatari, Y.O. / Tochio, N. / Nakanishi, T. / Miyamoto, K. / Li, H. / Kobayashi, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. ...Kamatari, Y.O. / Tochio, N. / Nakanishi, T. / Miyamoto, K. / Li, H. / Kobayashi, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of the UBA Domain of Human Tudor Domain Containing Protein 3 Authors: Kamatari, Y.O. / Tochio, N. / Nakanishi, T. / Miyamoto, K. / Li, H. / Kobayashi, N. / Tomizawa, T. / Koshiba, S. / 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 | 1wji.cif.gz | 346.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wji.ent.gz | 289.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wji_validation.pdf.gz | 341.1 KB | Display | wwPDB validaton report |
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Full document | 1wji_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 1wji_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 1wji_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/1wji ftp://data.pdbj.org/pub/pdb/validation_reports/wj/1wji | 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: 6436.161 Da / Num. of mol.: 1 / Fragment: UBA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: IMS cDNA CAE03871 / Plasmid: P040301-26 / References: UniProt: Q9H7E2 |
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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: 1.04mM UBA domain U-13C, 15N; 20mM d-Tris-HCl buffer (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / 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: 800 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 |