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- PDB-5oke: Conservatively refined structure of Gan1D-E170Q, a catalytic muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oke | |||||||||
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Title | Conservatively refined structure of Gan1D-E170Q, a catalytic mutant of a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with cellobiose-6-phosphate | |||||||||
![]() | Putative 6-phospho-beta-galactobiosidase | |||||||||
![]() | HYDROLASE / 6-phospho-beta-galactosidase / Geobacillus stearothermophilus / Glycoside Hydrolase / GH1 family | |||||||||
Function / homology | ![]() 6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / carbohydrate catabolic process / beta-glucosidase activity / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G. | |||||||||
![]() | ![]() Title: Structural basis for enzyme bifunctionality - the case of Gan1D from Geobacillus stearothermophilus. Authors: Lansky, S. / Zehavi, A. / Belrhali, H. / Shoham, Y. / Shoham, 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 | ![]() | 817.6 KB | Display | ![]() |
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PDB format | ![]() | 674.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 87.8 KB | Display | |
Data in CIF | ![]() | 135.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ok7SC ![]() 5okaC ![]() 5okbC ![]() 5okgC ![]() 5okhC ![]() 5okjC ![]() 5okkC ![]() 5okqC ![]() 5okrC ![]() 5oksC 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 56208.730 Da / Num. of mol.: 4 / Mutation: E170Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: gan1D / Production host: ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/BG6.gif)
#2: Polysaccharide | #3: Sugar | |
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-Non-polymers , 3 types, 2211 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16-19% PEG 8K, 3% MPD, 0.1M imidazole buffer pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→36.14 Å / Num. obs: 478362 / % possible obs: 98.4 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.31→1.33 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 23286 / CC1/2: 0.7 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OK7 Resolution: 1.31→34.777 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31→34.777 Å
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Refine LS restraints |
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LS refinement shell |
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