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Yorodumi- PDB-2dbg: Solution structure of the Pyrin (PAAD-DAPIN) domain in human Myel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dbg | ||||||
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Title | Solution structure of the Pyrin (PAAD-DAPIN) domain in human Myeloid cell nuclear differentiation antigen | ||||||
Components | Myeloid cell nuclear differentiation antigen | ||||||
Keywords | IMMUNE SYSTEM / INTERFERON INDUCTION / DNA-BINDING / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of B cell proliferation / cellular response to interferon-beta / cellular defense response / activation of innate immune response / B cell receptor signaling pathway / azurophil granule lumen / double-stranded DNA binding / ficolin-1-rich granule lumen / positive regulation of apoptotic process / intracellular membrane-bounded organelle ...negative regulation of B cell proliferation / cellular response to interferon-beta / cellular defense response / activation of innate immune response / B cell receptor signaling pathway / azurophil granule lumen / double-stranded DNA binding / ficolin-1-rich granule lumen / positive regulation of apoptotic process / intracellular membrane-bounded organelle / DNA damage response / Neutrophil degranulation / nucleolus / extracellular exosome / extracellular region / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Saito, K. / Inoue, M. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the Pyrin (PAAD-DAPIN) domain in human Myeloid cell nuclear differentiation antigen Authors: Saito, K. / Inoue, M. / Koshiba, S. / 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 | 2dbg.cif.gz | 635.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dbg.ent.gz | 532.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dbg_validation.pdf.gz | 344.9 KB | Display | wwPDB validaton report |
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Full document | 2dbg_full_validation.pdf.gz | 469.6 KB | Display | |
Data in XML | 2dbg_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 2dbg_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/2dbg ftp://data.pdbj.org/pub/pdb/validation_reports/db/2dbg | 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: 11510.404 Da / Num. of mol.: 1 / Fragment: PYRIN DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: AB1735_E12 / Plasmid: P050613-16 / Production host: Cell free synthesis / References: UniProt: P41218 |
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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 protein, 20mM d-tris-HCl, pH7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120 / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 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: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |