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- PDB-6z39: Structure of recombinant human beta-glucocerebrosidase in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6z39 | ||||||
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Title | Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY functionalised epoxide activity based probe | ||||||
![]() | Glucosylceramidase![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
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 | ![]() | 428.1 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 ![]() 6z3iC ![]() 2nt0S 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | ![]() Mass: 55640.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Recombinan beta-glucocerebrosidase (Cerezyme) missing the 40 amino acid signalling sequence Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P04062, ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | ![]() #3: Sugar | ![]() |
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-Non-polymers , 8 types, 944 molecules ![](data/chem/img/Q65.gif)
![](data/chem/img/K35.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GAI.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K35.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GAI.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-Q65 / ( | ||||||||||||
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#5: Chemical | #6: Chemical | ChemComp-SO4 / ![]() #7: Chemical | ChemComp-EDO / ![]() #8: Chemical | ChemComp-GOL / ![]() #9: Chemical | ChemComp-GAI / | ![]() #10: Chemical | ChemComp-ACT / | ![]() #11: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.34 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.95 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.6 |
-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: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→103.82 Å / Num. obs: 159511 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2 / Num. unique obs: 7828 / CC1/2: 0.761 / Rpim(I) all: 0.445 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2NT0 Resolution: 1.7→103.816 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.166 / WRfactor Rwork: 0.149 / SU B: 2.314 / SU ML: 0.068 / Average fsc free: 0.872 / Average fsc work: 0.8789 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.077 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: 23.297 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→103.816 Å
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Refine LS restraints |
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LS refinement shell |
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