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Yorodumi- PDB-2dzj: 2DZJ/Solution Structure of the N-terminal Ubiquitin-like Domain i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dzj | ||||||
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Title | 2DZJ/Solution Structure of the N-terminal Ubiquitin-like Domain in Human Synaptic Glycoprotein SC2 | ||||||
Components | Synaptic glycoprotein SC2 | ||||||
Keywords | SUGAR BINDING PROTEIN / synaptic glycoprotein SC2 / ubiquitin-like fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information very-long-chain enoyl-CoA reductase / very-long-chain enoyl-CoA reductase activity / long-chain fatty-acyl-CoA biosynthetic process / Synthesis of very long-chain fatty acyl-CoAs / very long-chain fatty acid biosynthetic process / very-long-chain fatty acyl-CoA dehydrogenase activity / sphingolipid metabolic process / fatty acid elongation / oxidoreductase activity / endoplasmic reticulum membrane ...very-long-chain enoyl-CoA reductase / very-long-chain enoyl-CoA reductase activity / long-chain fatty-acyl-CoA biosynthetic process / Synthesis of very long-chain fatty acyl-CoAs / very long-chain fatty acid biosynthetic process / very-long-chain fatty acyl-CoA dehydrogenase activity / sphingolipid metabolic process / fatty acid elongation / oxidoreductase activity / endoplasmic reticulum membrane / endoplasmic reticulum / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Zhao, C. / Yoneyama, M. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: 2DZJ/Solution Structure of the N-terminal Ubiquitin-like Domain in Human Synaptic Glycoprotein SC2 Authors: Zhao, C. / Yoneyama, M. / Koshiba, S. / Watanabe, S. / Harada, T. / 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 | 2dzj.cif.gz | 547.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dzj.ent.gz | 461 KB | Display | PDB format |
PDBx/mmJSON format | 2dzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dzj_validation.pdf.gz | 341.3 KB | Display | wwPDB validaton report |
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Full document | 2dzj_full_validation.pdf.gz | 475.1 KB | Display | |
Data in XML | 2dzj_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 2dzj_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/2dzj ftp://data.pdbj.org/pub/pdb/validation_reports/dz/2dzj | 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: 10005.466 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: GPSN2 / Plasmid: P060522-14 / References: UniProt: Q9NZ01 |
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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: 1.10mM ubiquitin-like domain U-15N, 13C; 20mM d-Tris-HCl (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: 296.0 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-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 |