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- PDB-1qwn: GOLGI ALPHA-MANNOSIDASE II Covalent Intermediate Complex with 5-f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qwn | |||||||||
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Title | GOLGI ALPHA-MANNOSIDASE II Covalent Intermediate Complex with 5-fluoro-gulosyl-fluoride | |||||||||
![]() | Alpha-mannosidase II | |||||||||
![]() | HYDROLASE / N-TERMINAL ALPHA-BETA DOMAIN / THREE HELIX BUNDLE / 2 C-TERMINAL BETA BARRELS / Family 38 Glycosyl hydrolase | |||||||||
Function / homology | ![]() 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 / mannose metabolic process / N-glycan processing / 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 / mannose metabolic process / N-glycan processing / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / lysosome / Golgi membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Numao, S. / Kuntz, D.A. / Withers, S.G. / Rose, D.R. | |||||||||
![]() | ![]() Title: Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates. Authors: Numao, S. / Kuntz, D.A. / Withers, S.G. / Rose, D.R. | |||||||||
History |
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Remark 999 | SEQUENCE The E -> K conflict for residue 970 is noted in Swiss-Prot entry Q24451. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.6 KB | Display | ![]() |
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PDB format | ![]() | 194.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 503.2 KB | Display | ![]() |
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Full document | ![]() | 516.5 KB | Display | |
Data in XML | ![]() | 47.6 KB | Display | |
Data in CIF | ![]() | 75.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qwuC ![]() 1qx1C ![]() 1htyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 119701.617 Da / Num. of mol.: 1 / Fragment: Family 38 catalytic domain (residues 94-1108) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/GUL.gif)
![](data/chem/img/GUL.gif)
#2: Sugar | ChemComp-NAG / |
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#4: Sugar | ChemComp-GUL / ( |
-Non-polymers , 4 types, 1037 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-TRS / |
#6: Chemical | ChemComp-MPD / ( |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.16 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, MPD, Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion / Details: van den Elsen, J.M., (2001) EMBO J., 20, 3008. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2002 / Details: monochromator |
Radiation | Monochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. all: 328509 / Num. obs: 317663 / % possible obs: 96.7 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.2→1.22 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 3.4 / % possible all: 91.4 |
Reflection | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 30 Å / Num. obs: 324605 / % possible obs: 98.8 % / Num. measured all: 2449245 |
Reflection shell | *PLUS % possible obs: 91.4 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1HTY Resolution: 1.2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 12.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.97 |