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Yorodumi- PDB-2d5u: Solution structure of the N-terminal portion of the PUB domain of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d5u | ||||||
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Title | Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase | ||||||
Components | N-glycanase 1 | ||||||
Keywords | HYDROLASE / PNGase | ||||||
Function / homology | Function and homology information peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / glycoprotein catabolic process / protein quality control for misfolded or incompletely synthesized proteins / collagen-containing extracellular matrix / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing | ||||||
Authors | Sasakawa, H. / Hirao, T. / Yamaguchi, Y. / Suzuki, T. / Kato, K. | ||||||
Citation | Journal: To be Published Title: Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase Authors: Sasakawa, H. / Hirao, T. / Yamaguchi, Y. / Suzuki, T. / Kato, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d5u.cif.gz | 428.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d5u.ent.gz | 362.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d5u ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d5u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13465.267 Da / Num. of mol.: 1 / Fragment: PUB domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codonplus References: GenBank: 31981178, UniProt: Q9JI78*PLUS, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 5 / pH: 5.0 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: distance geometry simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 1460 restraints, 1272 are NOE-derived distance constraints, 152 dihedral angle restraints, 36 distance restraints for hydrogen bonds. | ||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10 |