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- PDB-1qwu: Golgi alpha-mannosidase II D341N mutant complex with 5-F-guloside -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qwu | |||||||||
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Title | Golgi alpha-mannosidase II D341N mutant complex with 5-F-guloside | |||||||||
![]() | Alpha-mannosidase II | |||||||||
![]() | HYDROLASE / glycosyl hydrolase family 38 / covalent catalytic intermediate | |||||||||
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 | ![]() | 243.4 KB | Display | ![]() |
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PDB format | ![]() | 189.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.8 KB | Display | ![]() |
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Full document | ![]() | 495.9 KB | Display | |
Data in XML | ![]() | 46.5 KB | Display | |
Data in CIF | ![]() | 73.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qwnC ![]() 1qx1C ![]() 1htyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 119700.633 Da / Num. of mol.: 1 / Fragment: Family 38 catalytic domain (residues 94-1108) / Mutation: D341N 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 , 3 types, 1027 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-MPD / ( |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.83 % | ||||||||||||||||||||||||
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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: MARRESEARCH / Detector: IMAGE PLATE / Details: Osmic |
Radiation | Monochromator: focussing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 68690 / Num. obs: 66355 / % possible obs: 96.6 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 7.5 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.03→2.16 Å / Num. unique all: 10064 / % possible all: 92.4 |
Reflection | *PLUS Highest resolution: 2.03 Å / Num. obs: 68989 / % possible obs: 99.9 % / Num. measured all: 476418 |
Reflection shell | *PLUS Lowest resolution: 2.08 Å / % possible obs: 98.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1HTY Resolution: 2.03→19.84 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.5168 Å2 / ksol: 0.338431 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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