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Yorodumi- PDB-6rqz: GOLGI ALPHA-MANNOSIDASE II complex with Manno-epi-cyclophellitol ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rqz | ||||||||||||
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Title | GOLGI ALPHA-MANNOSIDASE II complex with Manno-epi-cyclophellitol aziridine | ||||||||||||
Components | Alpha-mannosidase 2 | ||||||||||||
Keywords | HYDROLASE / Mannosidase / Glycoside Hydrolase | ||||||||||||
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: 1.53 Å | ||||||||||||
Authors | Armstrong, Z. / Lahav, D. / Johnson, R. / Kuo, C.L. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / Debets, M. / van der Stelt, M. / Codee, J.D.C. ...Armstrong, Z. / Lahav, D. / Johnson, R. / Kuo, C.L. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / Debets, M. / van der Stelt, M. / Codee, J.D.C. / Aerts, J.M.F.G. / Wu, L. / Overkleeft, H.S. / Davies, G.J. | ||||||||||||
Funding support | United Kingdom, Netherlands, 3items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. Authors: Armstrong, Z. / Kuo, C.L. / Lahav, D. / Liu, B. / Johnson, R. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M.F. / Florea, B.I. / Hissink, C. / Boot, R.G. / ...Authors: Armstrong, Z. / Kuo, C.L. / Lahav, D. / Liu, B. / Johnson, R. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M.F. / Florea, B.I. / Hissink, C. / Boot, R.G. / Geurink, P.P. / Ovaa, H. / van der Stelt, M. / van der Marel, G.M. / Codee, J.D.C. / Aerts, J.M.F.G. / Wu, L. / Overkleeft, H.S. / Davies, G.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rqz.cif.gz | 247.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rqz.ent.gz | 188.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/6rqz ftp://data.pdbj.org/pub/pdb/validation_reports/rq/6rqz | HTTPS FTP |
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-Related structure data
Related structure data | 6rpcC 6rrhC 6rrjC 6rrnC 6rruC 6rrwC 6rrxC 6rryC 6rs0C 3bubS 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: 118208.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha-Man-IIa, GmII, CG18802 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase |
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-Non-polymers , 5 types, 816 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-SIN / | #4: Chemical | ChemComp-KGH / ( | #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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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: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10 % PEG 3,350, 0.1 M sodium succinate pH 7.0 with micro seeding |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→89.99 Å / Num. obs: 163365 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.999 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.53→1.56 Å / Num. unique all: 8006 / Num. unique obs: 8006 / CC1/2: 0.727 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BUB Resolution: 1.53→81.3 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 102.74 Å2 / Biso mean: 25.299 Å2 / Biso min: 14.42 Å2
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Refinement step | Cycle: final / Resolution: 1.53→81.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Total num. of bins used: 20
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