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Yorodumi- PDB-2cm0: The PUB domain functions as a p97 binding module in human peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cm0 | ||||||
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Title | The PUB domain functions as a p97 binding module in human peptide N-glycanase. | ||||||
Components | PEPTIDE N-GLYCANASE HOMOLOG | ||||||
Keywords | TRANSFERASE / KINASE / PUG DOMAIN | ||||||
Function / homology | Function and homology information peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / : / glycoprotein catabolic process / protein deglycosylation / protein quality control for misfolded or incompletely synthesized proteins / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / protein folding / metal ion binding / nucleus ...peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / : / glycoprotein catabolic process / protein deglycosylation / protein quality control for misfolded or incompletely synthesized proteins / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / protein folding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Allen, M.D. / Buchberger, A. / Bycroft, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: The Pub Domain Functions as a P97 Binding Module in Human Peptide N-Glycanase. Authors: Allen, M.D. / Buchberger, A. / Bycroft, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cm0.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cm0.ent.gz | 22.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/2cm0 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/2cm0 | HTTPS FTP |
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-Related structure data
Related structure data | 2ccqSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10915.451 Da / Num. of mol.: 1 / Fragment: PUG DOMAIN, RESIDUES 8-106 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9BVR8, UniProt: Q96IV0*PLUS |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-BME / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 38 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 47 TO ALA ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 49 % |
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Crystal grow | pH: 9.2 / Details: 50% PEG 400, 0.1M CHES, PH 9.5, 0.2M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Date: Apr 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24.48 Å / Num. obs: 8005 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CCQ Resolution: 1.9→25 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: DENSITY MODIFICATION / Bsol: 75.5379 Å2 / ksol: 0.407888 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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Xplor file |
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