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Yorodumi- PDB-3bvu: GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bvu | |||||||||
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Title | GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl(alpha-D-mannopyranosyl)-(1->3)-S-[(alpha-D-mannopyranosyl)-(1->6)]-alpha-D-mannopyranoside | |||||||||
Components | Alpha-mannosidase 2 | |||||||||
Keywords | HYDROLASE / FAMILY 38 GLYCOYSL HYDROLASE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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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Remark 999 | SEQUENCE E970K conflict in UNP entry Q24451 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bvu.cif.gz | 501.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bvu.ent.gz | 405.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/3bvu ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bvu | HTTPS FTP |
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-Related structure data
Related structure data | 3bubC 3budC 3buiC 3bupC 3buqC 3bvtC 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 , 1 types, 1 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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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl 3-thio-alpha-D-mannopyranoside / methyl alpha-D-mannopyranosyl-(1->3)-[alpha-D-mannopyranosyl-(1->6)]-3-thio-alpha-D-mannopyranoside Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 534.530 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: oligosaccharide with S-glycosidic bond between monosaccharides, and with branches References: methyl alpha-D-mannopyranosyl-(1->3)-[alpha-D-mannopyranosyl-(1->6)]-3-thio-alpha-D-mannopyranoside |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 1502 molecules
#4: Chemical | ChemComp-PO4 / |
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#5: Chemical | ChemComp-ZN / |
#6: Chemical | ChemComp-MRD / ( |
#7: Water | ChemComp-HOH / |
-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: 44.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: TRIS, NACL, PEG6000, MPD. Crystals washed in phosphate buffered reservoir solution before soaking with substrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.12→20 Å / Num. all: 401972 / Num. obs: 399962 / % possible obs: 99.5 % / Observed criterion σ(F): 0.142 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.077 / Χ2: 1.028 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.12→1.15 Å / Redundancy: 5 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.5 / Num. unique all: 26166 / Χ2: 0.976 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HTY Resolution: 1.12→20 Å / Num. parameters: 105262 / Num. restraintsaints: 111845 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.031
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.609 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.128 Å | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→20 Å
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Refine LS restraints |
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