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- PDB-3bvw: GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex w... -
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Basic information
Entry | Database: PDB / ID: 3bvw | ||||||||||||
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Title | GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl (2-deoxy-2-acetamido-beta-D-glucopyranosyl)-(1->2)-ALPHA-D-mannopyranosyl- (1->3)-[ALPHA-D-mannopyranosyl-(1->6)-6-thio-alpha-D-mannopyranosyl- (1->6)]-BETA-D-mannopyranoside | ||||||||||||
![]() | Alpha-mannosidase 2 | ||||||||||||
![]() | HYDROLASE / FAMILY 38 GLYCOYSL HYDROLASE / Glycosidase / Golgi apparatus / Membrane / Signal-anchor / Transmembrane | ||||||||||||
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 glycosylation / carbohydrate binding / Golgi membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kuntz, D.A. / Rose, D.R. | ||||||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 497.1 KB | Display | ![]() |
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PDB format | ![]() | 402.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bubC ![]() 3budC ![]() 3buiC ![]() 3bupC ![]() 3buqC ![]() 3bvtC ![]() 3bvuC ![]() 3bvvC ![]() 3bvxC ![]() 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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Unit cell |
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Components
#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.) ![]() ![]() ![]() ![]() References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-6-thio-alpha-D-mannopyranose-(1-6)]methyl beta-D-mannopyranoside / methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->2)-alpha-D-mannopyranosyl-(1->3)-[alpha-D- ...methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->2)-alpha-D-mannopyranosyl-(1->3)-[alpha-D-mannopyranosyl-(1->6)-6-thio -alpha-D-mannopyranosyl-(1->6)]-beta-D-mannopyranoside![]() Source method: isolated from a genetically manipulated source Details: oligosaccharide with S-glycosidic bond between monosaccharides, and with branches References: methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->2)-alpha-D-mannopyranosyl-(1->3)-[alpha-D-mannopyranosyl-(1->6)-6-thio -alpha-D-mannopyranosyl-(1->6)]-beta-D-mannopyranoside |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
Sequence details | E970K CONFLICT IN UNP ENTRY Q24451 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: TRIS, NACL, PEG6000, MPD. Crystals washed in MOPS buffered reservoir solution before soaking with substrate for 24 hrs., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 324471 / Num. obs: 318631 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.2 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HTY Resolution: 1.2→10 Å / Num. parameters: 89561 / Num. restraintsaints: 112307 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.041. Density for second mannose is too weak to assign accurately. Occupancy has been set to zero to denote this.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.369 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.135 Å | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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