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- PDB-6z3i: Structure of recombinant beta-glucocerebrosidase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6z3i | ||||||
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Title | Structure of recombinant beta-glucocerebrosidase in complex with bifunctional cyclophellitol aziridine activity based probe | ||||||
![]() | Lysosomal acid glucosylceramidase | ||||||
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Function / homology | ![]() positive regulation of protein lipidation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rowland, R.J. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design, Synthesis and Structural Analysis of Glucocerebrosidase Imaging Agents. Authors: Rowland, R.J. / Chen, Y. / Breen, I. / Wu, L. / Offen, W.A. / Beenakker, T.J. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Aerts, J.M.F.G. / Artola, M. / Overkleeft, H.S. / Davies, G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ytpC ![]() 6ytrC ![]() 6yutC ![]() 6yv3C ![]() 6z39C ![]() 6tjkS 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules BBB
#1: Protein | Mass: 55659.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Recombinant human beta-glucocerebrosidase lacking its 40 amino acid signalling sequence produced in insect cells Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P04062, ![]() ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
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#4: Sugar | ![]() |
-Non-polymers , 4 types, 359 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/Q68.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/Q68.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / ![]() #5: Chemical | ChemComp-EDO / ![]() #6: Chemical | ChemComp-Q68 / ~{ | #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Na2SO4, 0.25 M HEPES pH 7, PEG3350 14%, 1:1000 seed |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→76.67 Å / Num. obs: 49541 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.084 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.351 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2966 / CC1/2: 0.506 / Rpim(I) all: 1.301 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6TJK Resolution: 1.8→66.578 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.163 / SU B: 3.598 / SU ML: 0.098 / Average fsc free: 0.8785 / Average fsc work: 0.8756 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.107 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.448 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→66.578 Å
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Refine LS restraints |
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LS refinement shell |
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