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Yorodumi- PDB-3bvv: Golgi mannosidase II D204A catalytic nucleophile mutant complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bvv | ||||||||||||
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Title | Golgi mannosidase II D204A catalytic nucleophile mutant complex with METHYL ALPHA-D-MANNOPYRANOSYL-(1->3)-[6-THIO-ALPHA-D-MANNOPYRANOSYL-(1->6)]-BETA-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: 1.3 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bvv.cif.gz | 502.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bvv.ent.gz | 407.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/3bvv ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bvv | HTTPS FTP |
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-Related structure data
Related structure data | 3bubC 3budC 3buiC 3bupC 3buqC 3bvtC 3bvuC 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 / Sugars , 2 types, 2 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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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[6-thio-alpha-D-mannopyranose-(1-6)]methyl beta-D-mannopyranoside Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 1662 molecules
#3: Chemical | ChemComp-PO4 / | ||
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#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | ChemComp-MRD / ( | ||
#6: Chemical | #7: 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: 2.21 Å3/Da / Density % sol: 44.31 % |
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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 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: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.972 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. all: 260486 / Num. obs: 254755 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.8 / % possible all: 78.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HTY Resolution: 1.3→19.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.292 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.046 / Stereochemistry target values: Engh & Huber / 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 mean: 16.368 Å2
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Refine analyze | Luzzati coordinate error obs: 0.135 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→19.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.332 Å / Total num. of bins used: 20
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