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- PDB-5oks: Non-conservatively refined structure of Gan1D, a 6-phospho-beta-g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oks | ||||||
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Title | Non-conservatively refined structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-beta-glucose | ||||||
![]() | Putative 6-phospho-beta-galactobiosidase | ||||||
![]() | HYDROLASE / 6-phospho-beta-galactosidase / GH1 / glycoside hydrolase / 6-phospho-beta-glucose | ||||||
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 | ![]() | 214.8 KB | Display | ![]() |
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PDB format | ![]() | 169.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 39.4 KB | Display | |
Data in CIF | ![]() | 57.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ok7C ![]() 5okaC ![]() 5okbC ![]() 5okeC ![]() 5okgC ![]() 5okhSC ![]() 5okjC ![]() 5okkC ![]() 5okqC ![]() 5okrC 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
#1: Protein | Mass: 56209.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: gan1D / Production host: ![]() ![]() #2: Sugar | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-IMD / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16-19% PEG 8K, 0.1M imidazole buffer pH 6.5, 3% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→27.88 Å / Num. obs: 70701 / % possible obs: 89.6 % / Redundancy: 3.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.118 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.96→2 Å / Rmerge(I) obs: 1.027 / Mean I/σ(I) obs: 1 / Num. unique obs: 2275 / CC1/2: 0.503 / % possible all: 45.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OKH Resolution: 1.96→27.88 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→27.88 Å
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Refine LS restraints |
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LS refinement shell |
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