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- PDB-4zoc: Crystal Structure of mutant (D270A) beta-glucosidase from Listeri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zoc | ||||||
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Title | Crystal Structure of mutant (D270A) beta-glucosidase from Listeria innocua in complex with sophorotriose | ||||||
![]() | 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 | ![]() | 612.1 KB | Display | ![]() |
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PDB format | ![]() | 500.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zo6C ![]() 4zo7C ![]() 4zo8C ![]() 4zo9C ![]() 4zoaC ![]() 4zobC ![]() 4zodC ![]() 4zoeSC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 724 / Label seq-ID: 1 - 724
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Components
#1: Protein | Mass: 80572.031 Da / Num. of mol.: 2 / Mutation: K2E, D270A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CLIP 11262 / Gene: lin1840 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.89 % |
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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: May 26, 2014 |
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: 1.79→32.5 Å / Num. obs: 166046 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 8.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4ZOE Resolution: 1.79→32.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.56 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.101 / 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: 88.75 Å2 / Biso mean: 15.084 Å2 / Biso min: 4.19 Å2
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Refinement step | Cycle: final / Resolution: 1.79→32.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 46275 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.791→1.837 Å / Total num. of bins used: 20
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