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Yorodumi- PDB-5k6n: Structure of a GH3 b-glicosidase from cow rumen metagenome in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k6n | |||||||||
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Title | Structure of a GH3 b-glicosidase from cow rumen metagenome in complexed with xylose | |||||||||
Components | B-GLUCOSIDASE | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / METAGENOME / B-GLICOSIDASE / FUNCTIONAL FOOD / PREBIOTICS / MICROBIOTA / XYLOSE | |||||||||
Function / homology | beta-D-xylopyranose Function and homology information | |||||||||
Biological species | metagenome (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k6n.cif.gz | 173.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k6n.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 5k6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k6n_validation.pdf.gz | 464.6 KB | Display | wwPDB validaton report |
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Full document | 5k6n_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 5k6n_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 5k6n_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/5k6n ftp://data.pdbj.org/pub/pdb/validation_reports/k6/5k6n | HTTPS FTP |
-Related structure data
Related structure data | 5k6lSC 5k6mC 5k6oC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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): Rosetta 2 | ||||
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#2: Sugar | ChemComp-XYP / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.67 % / Description: diamond-shaped crystal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, then soaked in 50mM xylose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→95.04 Å / Num. obs: 58135 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.08→2.14 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K6L Resolution: 2.08→95.04 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.029 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.155 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.14 Å2
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Refinement step | Cycle: 1 / Resolution: 2.08→95.04 Å
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Refine LS restraints |
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