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Open data
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Basic information
Entry | Database: PDB / ID: 8pej | |||||||||
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Title | CjGH35 with a Galactosidase Activity-Based Probe | |||||||||
![]() | Beta-galactosidase, putative, bgl35A | |||||||||
![]() | HYDROLASE / Beta-galactosidase / Complex / Activity-based Probe | |||||||||
Function / homology | ![]() beta-galactosidase complex / beta-galactosidase / vacuole / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Offen, W.A. / Davies, G.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The development of a broad-spectrum retaining beta-exo-galactosidase activity-based probe. Authors: Kuo, C.L. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Beenakker, T.J.M. / Offen, W.A. / Willems, L.I. / Boot, R.G. / Sarris, A.J. / Marques, A.R.A. / Codee, J.D.C. / van der Marel, G.A. / ...Authors: Kuo, C.L. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Beenakker, T.J.M. / Offen, W.A. / Willems, L.I. / Boot, R.G. / Sarris, A.J. / Marques, A.R.A. / Codee, J.D.C. / van der Marel, G.A. / Florea, B.I. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.F.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.7 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 187 KB | Display | |
Data in CIF | ![]() | 285.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 62127.023 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: beta-galactosidase without signal peptide and with N-terminal hexahistidine tag Source: (gene. exp.) ![]() Gene: bgl35A, CJA_2707 / Production host: ![]() ![]() #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-YGX / ( #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→99.32 Å / Num. obs: 802827 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.043 / Rrim(I) all: 0.061 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.0467 / Mean I/σ(I) obs: 2 / Num. unique obs: 37248 / CC1/2: 0.719 / Rpim(I) all: 0.0467 / Rrim(I) all: 0.66 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions There was incomplete electron density for loop 434 - 445, which has been modelled at partial occupancy or left partially unmodelled for each chain.
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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: 21.647 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→82.544 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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