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- PDB-3eqo: Crystal structure of beta-1,3-glucanase from Phanerochaete chryso... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eqo | |||||||||
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Title | Crystal structure of beta-1,3-glucanase from Phanerochaete chrysosporium (Lam55A) gluconolactone complex | |||||||||
![]() | Glucan 1,3-beta-glucosidase | |||||||||
![]() | HYDROLASE / tandem beta-helix domains / Glycosidase | |||||||||
Function / homology | ![]() glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / polygalacturonase activity / metabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ishida, T. / Fushinobu, S. / Kawai, R. / Kitaoka, M. / Igarashi, K. / Samejima, M. | |||||||||
![]() | ![]() Title: Crystal structure of glycoside hydrolase family 55 beta -1,3-glucanase from the basidiomycete Phanerochaete chrysosporium Authors: Ishida, T. / Fushinobu, S. / Kawai, R. / Kitaoka, M. / Igarashi, K. / Samejima, M. #1: Journal: Biotechnol.Lett. / Year: 2006 Title: Gene cloning and heterologous expression of glycoside hydrolase family 55 beta-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium Authors: Kawai, R. / Igarashi, K. / Samejima, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.8 KB | Display | ![]() |
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PDB format | ![]() | 250.3 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 | ![]() | 63.7 KB | Display | |
Data in CIF | ![]() | 95.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eqnSC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 80112.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: 2.89 Å3/Da / Density % sol: 57.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 15% PEG 3350, 0.1M zinc acetate, 0.05M MES-NaOH, 10% glycerol, 2% ethanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2006 |
Radiation | Monochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 84385 / Num. obs: 77511 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.097 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.257 / % possible all: 74.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3EQN Resolution: 2.25→31.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.338 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.031 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→31.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.254→2.312 Å / Total num. of bins used: 20
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