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- PDB-5oss: Beta-glucosidase from Thermotoga maritima in complex with Gluco-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oss | ||||||
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Title | Beta-glucosidase from Thermotoga maritima in complex with Gluco-1H-imidazole | ||||||
![]() | Beta-glucosidase A | ||||||
![]() | HYDROLASE / glycosylhydrolase / Thermotoga maritima / glucoimidazole | ||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Offen, W.A. / Schroeder, S.P. / Davies, G.J. / Overkleeft, H.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Gluco-1 H-imidazole: A New Class of Azole-Type beta-Glucosidase Inhibitor. Authors: Schroder, S.P. / Wu, L. / Artola, M. / Hansen, T. / Offen, W.A. / Ferraz, M.J. / Li, K.Y. / Aerts, J.M.F.G. / van der Marel, G.A. / Codee, J.D.C. / Davies, G.J. / Overkleeft, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.3 KB | Display | ![]() |
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PDB format | ![]() | 158.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.1 KB | Display | ![]() |
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Full document | ![]() | 482.7 KB | Display | |
Data in XML | ![]() | 36.8 KB | Display | |
Data in CIF | ![]() | 53.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ostC ![]() 1od0S S: Starting model for refinement C: citing same article ( |
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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, 2 molecules AB
#1: Protein | Mass: 53940.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: bglA / Plasmid: pET28a / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 380 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/AEZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/AEZ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-AEZ / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: PEG 4000, imidazole, calcium acetate, trimethylamine oxide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→72.77 Å / Num. obs: 112065 / % possible obs: 100 % / Redundancy: 12.6 % / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 12.9 % / Rmerge(I) obs: 2.812 / Num. unique obs: 5461 / CC1/2: 0.61 / Rpim(I) all: 0.831 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OD0.PDB Resolution: 1.7→72.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.499 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS UNMODELLED DENSITY NEAR HIS180A AND TWO ETHYLENE GLYCOL MOLECULES HAVE BEEN MODELLED AT PARTIAL OCCUPANCY BETWEEN GLU351A AND GLU405A.
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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: 36.313 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→72.77 Å
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Refine LS restraints |
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