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Yorodumi- PDB-1g6i: Crystal structure of the yeast alpha-1,2-mannosidase with bound 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g6i | |||||||||
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Title | Crystal structure of the yeast alpha-1,2-mannosidase with bound 1-deoxymannojirimycin at 1.59 A resolution | |||||||||
Components | CLASS I ALPHA-1,2-MANNOSIDASE | |||||||||
Keywords | HYDROLASE / alpha-alpha7 barrel | |||||||||
Function / homology | Function and homology information protein deglycosylation involved in glycoprotein catabolic process / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / protein glycosylation / : / carbohydrate metabolic process / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.59 Å | |||||||||
Authors | Herscovics, A. / Lipari, F. / Sleno, B. / Romera, P.A. / Vallee, F. / Yip, P. / Howell, P.A. | |||||||||
Citation | Journal: CARBOHYDRATE BIOENGINEERING. INTERDISCIPLINARY APPROACHES. Year: 2002 Title: Structure and function of Class I a1,2-mannosidases involved in glycoprotein biosynthesis. Authors: Herscovics, A. / Lipari, F. / Sleno, B. / Romera, P.A. / Vallee, F. / Yip, P. / Howell, P.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g6i.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g6i.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 1g6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g6i ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g6i | 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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Unit cell |
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Details | The protein is active as a monomer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 62632.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MNS1 / Plasmid: YPHDELTA33 / Production host: Pichia pastoris (fungus) References: UniProt: P32906, mannosyl-oligosaccharide 1,2-alpha-mannosidase |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 417 molecules
#5: Chemical | ChemComp-CA / |
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#6: Chemical | ChemComp-DMJ / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG MME 2K, Sodium Citrate, Ammonium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 1999 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→500 Å / Num. all: 590345 / Num. obs: 590345 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.59→1.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / Num. unique all: 13423 / Rsym value: 0.17 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: Ab initio Resolution: 1.59→33.56 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: NO
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Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.59→33.56 Å
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Refine LS restraints |
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