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Yorodumi- PDB-3ejp: Golgi alpha-Mannosidase II in complex with 5-substituted swainson... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ejp | ||||||
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Title | Golgi alpha-Mannosidase II in complex with 5-substituted swainsonine analog: (5R)-5-[2'-oxo-2'-(phenyl)ethyl]-swainsonine | ||||||
Components | Alpha-mannosidase 2 | ||||||
Keywords | HYDROLASE / GH38 Glycosidase / Glycosidase / Golgi apparatus / Membrane / Metal-binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å | ||||||
Authors | Kuntz, D.A. / Rose, D.R. | ||||||
Citation | Journal: Chembiochem / Year: 2010 Title: Structural Investigation of the Binding of 5-Substituted Swainsonine Analogues to Golgi alpha-Mannosidase II. Authors: Kuntz, D.A. / Nakayama, S. / Shea, K. / Hori, H. / Uto, Y. / Nagasawa, H. / Rose, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ejp.cif.gz | 473.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ejp.ent.gz | 384.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ejp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/3ejp ftp://data.pdbj.org/pub/pdb/validation_reports/ej/3ejp | HTTPS FTP |
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-Related structure data
Related structure data | 3ejqC 3ejrC 3ejsC 3ejtC 3ejuC 3bubS 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: 119701.617 Da / Num. of mol.: 1 / Fragment: Catalytic domain; UNP residues 76-1108 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, 1298 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-MRD / ( |
#5: Chemical | ChemComp-HN2 / |
#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: 2.2 Å3/Da / Density % sol: 44.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 11, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9186 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→30 Å / Num. all: 247309 / Num. obs: 241556 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.04 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.32→1.34 Å / Redundancy: 3.21 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.46 / Num. unique all: 5479 / % possible all: 87.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BUB Resolution: 1.32→29.22 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.165 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.905 / SU B: 1.47 / SU ML: 0.028 / SU R Cruickshank DPI: 0.058 / SU Rfree: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.052 / 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 max: 69.76 Å2 / Biso mean: 15.273 Å2 / Biso min: 5.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→29.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.354 Å / Total num. of bins used: 20
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