[English] 日本語
Yorodumi- PDB-5k6o: Structure of a GH3 b-glucosidase from cow rumen metagenome in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k6o | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a GH3 b-glucosidase from cow rumen metagenome in complex with galactose | ||||||
Components | B-GLUCOSIDASEBeta-glucosidase | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / METAGENOME / B-GLICOSIDASE / FUNCTIONAL FOOD / PREBIOTICS / MICROBIOTA / GALACTOSE | ||||||
Function / homology | beta-D-galactopyranose Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Ramirez-Escudero, M. / Sanz-Aparicio, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural and Functional Characterization of a Ruminal beta-Glycosidase Defines a Novel Subfamily of Glycoside Hydrolase Family 3 with Permuted Domain Topology. Authors: Ramirez-Escudero, M. / Del Pozo, M.V. / Marin-Navarro, J. / Gonzalez, B. / Golyshin, P.N. / Polaina, J. / Ferrer, M. / Sanz-Aparicio, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5k6o.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5k6o.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 5k6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/5k6o ftp://data.pdbj.org/pub/pdb/validation_reports/k6/5k6o | HTTPS FTP |
---|
-Related structure data
Related structure data | 5k6lSC 5k6mC 5k6nC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 101951.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: cow rumen / Source: (gene. exp.) metagenome (others) / Gene: glyA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: beta-glucosidase | ||||
---|---|---|---|---|---|
#2: Sugar | ChemComp-GAL / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % / Description: Diamond-shaped crystal |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, then soaked in 100mM galactose. PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.1271 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→95.08 Å / Num. obs: 44188 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K6L Resolution: 2.29→95.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.988 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.334 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.29→95.07 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|