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Open data
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Basic information
Entry | Database: PDB / ID: 4zoe | ||||||
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Title | Crystal Structure of beta-glucosidase from Listeria innocua | ||||||
![]() | Lin1840 protein | ||||||
![]() | HYDROLASE / TIM barrel / beta-1 / 2-glucan degradation / cytosol | ||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Listeria innocua serovar 6a | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Nakajima, M. / Yoshida, R. / Miyanaga, A. / Abe, K. / Takahashi, Y. / Sugimoto, N. / Toyoizumi, H. / Nakai, H. / Kitaoka, M. / Taguchi, H. | ||||||
![]() | ![]() Title: Functional and Structural Analysis of a beta-Glucosidase Involved in beta-1,2-Glucan Metabolism in Listeria innocua Authors: Nakajima, M. / Yoshida, R. / Miyanaga, A. / Abe, K. / Takahashi, Y. / Sugimoto, N. / Toyoizumi, H. / Nakai, H. / Kitaoka, M. / Taguchi, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 599.1 KB | Display | ![]() |
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PDB format | ![]() | 492.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 461.9 KB | Display | |
Data in XML | ![]() | 60.3 KB | Display | |
Data in CIF | ![]() | 91.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zo6C ![]() 4zo7C ![]() 4zo8C ![]() 4zo9C ![]() 4zoaC ![]() 4zobC ![]() 4zocC ![]() 4zodC ![]() 1ex1S 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: 80616.039 Da / Num. of mol.: 2 / Mutation: K2E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CLIP 11262 / Gene: lin1840 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, NaCl, LiSO4, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2012 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.38 Å / Num. obs: 163230 / % possible obs: 98.5 % / Redundancy: 4.9 % / Net I/σ(I): 8.2 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EX1 Resolution: 1.8→28.17 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.045 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 74.22 Å2 / Biso mean: 14.86 Å2 / Biso min: 2.39 Å2
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Refinement step | Cycle: final / Resolution: 1.8→28.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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