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Yorodumi- PDB-3bud: Golgi mannosidase II D204A catalytic nucleophile mutant with an e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bud | ||||||
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Title | Golgi mannosidase II D204A catalytic nucleophile mutant with an empty active site | ||||||
Components | Alpha-mannosidase 2 | ||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE FAMILY 38 / Glycosidase / Golgi apparatus / Membrane / Signal-anchor / Transmembrane | ||||||
Function / homology | Function and homology information mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack ...mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / Golgi membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Kuntz, D.A. / Rose, D.R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant. Authors: Zhong, W. / Kuntz, D.A. / Ember, B. / Singh, H. / Moremen, K.W. / Rose, D.R. / Boons, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bud.cif.gz | 260.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bud.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3bud ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3bud | HTTPS FTP |
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-Related structure data
Related structure data | 3bubC 3buiC 3bupC 3buqC 3bvtC 3bvuC 3bvvC 3bvwC 3bvxC 1htyS 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 119657.602 Da / Num. of mol.: 1 / Fragment: Catalytic domain; UNP residues 76-1108 / Mutation: D204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha-Man-II, GmII / Plasmid: pMTBIP_NHIS / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 1503 molecules
#3: Chemical | ChemComp-PO4 / | ||
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#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | E970K CONFLICT IN UNP ENTRY Q24451 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Tris, NaCl, PEG6000, MPD; Tris found in the active site under normal crystallization conditions was removed by soaking crystals in phosphate buffered resevoir solution, pH 7.0, VAPOR ...Details: Tris, NaCl, PEG6000, MPD; Tris found in the active site under normal crystallization conditions was removed by soaking crystals in phosphate buffered resevoir solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 12, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 90096 / Num. obs: 89372 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.054 / Χ2: 0.998 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5801 / Χ2: 1.066 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HTY Resolution: 1.85→19.98 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.594 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.932 Å2
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Refine analyze | Luzzati coordinate error obs: 0.167 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.897 Å / Total num. of bins used: 20
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