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Yorodumi- PDB-1v2y: Solution Structure of Mouse Hypothetical Gene (RIKEN cDNA 3300001... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v2y | ||||||
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Title | Solution Structure of Mouse Hypothetical Gene (RIKEN cDNA 3300001G02) Product Homologous to Ubiquitin Fold | ||||||
Components | 3300001G02Rik protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / Ubiquitin-like fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information mRNA Splicing - Minor Pathway / U12-type spliceosomal complex / intercellular bridge / mRNA splicing, via spliceosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Zhao, C. / Kigawa, T. / Tomizawa, T. / Koshiba, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of Mouse Hypothetical Gene (RIKEN cDNA 3300001G02) Product Homologous to Ubiquitin Fold Authors: Zhao, C. / Kigawa, T. / Tomizawa, T. / Koshiba, S. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX determination method: author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v2y.cif.gz | 649.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v2y.ent.gz | 539.4 KB | Display | PDB format |
PDBx/mmJSON format | 1v2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v2y_validation.pdf.gz | 344.4 KB | Display | wwPDB validaton report |
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Full document | 1v2y_full_validation.pdf.gz | 505.4 KB | Display | |
Data in XML | 1v2y_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 1v2y_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/1v2y ftp://data.pdbj.org/pub/pdb/validation_reports/v2/1v2y | 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: 11792.489 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like Fold Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 3300001G02 / Plasmid: P030224-02 / References: UniProt: Q8VIK1 |
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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: 0.55mM protein U-15N, 13C; 20mM phosphate buffer NA (pH6.0); 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: 6.0 / Pressure: ambient / Temperature: 298.0 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, restrained molecular 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 |