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- PDB-6hpd: The structure of a beta-glucuronidase from glycoside hydrolase fa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hpd | ||||||
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Title | The structure of a beta-glucuronidase from glycoside hydrolase family 2 | ||||||
![]() | Beta-galactosidase (GH2) | ||||||
![]() | HYDROLASE / GH2 / glycoside hydrolase / glucuronidase | ||||||
Function / homology | ![]() beta-glucuronidase / beta-glucuronidase activity / periplasmic space / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Robb, C.S. / Gerlach, N. / Reisky, L. / Bornshoeru, U. / Hehemann, J.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, ...Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, M.D. / Trautwein-Schult, A. / Becher, D. / Schweder, T. / Bornscheuer, U.T. / Hehemann, J.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 | ![]() | 212.7 KB | Display | ![]() |
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PDB format | ![]() | 165.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.1 KB | Display | ![]() |
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Full document | ![]() | 427.6 KB | Display | |
Data in XML | ![]() | 36.8 KB | Display | |
Data in CIF | ![]() | 54.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hhmC ![]() 6hhnC ![]() 6hr5C ![]() 5dmyS 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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Unit cell |
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Components
#1: Protein | Mass: 112855.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-BR / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium Bromide, 0.1M BIS-TRIS pH 7.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→96.2 Å / Num. obs: 37999 / % possible obs: 99.5 % / Redundancy: 10 % / Biso Wilson estimate: 19.57 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.43→2.52 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 3961 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5dmy Resolution: 2.43→96.2 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / ESU R: 0.597 / ESU R Free: 0.248 / 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: 25.334 Å2
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Refinement step | Cycle: 1 / Resolution: 2.43→96.2 Å
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Refine LS restraints |
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