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Yorodumi- PDB-5k6m: Structure of a GH3 b-glIcosidase from cow rumen metagenome in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k6m | ||||||
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Title | Structure of a GH3 b-glIcosidase from cow rumen metagenome in complex with glucose | ||||||
Components | B-GLUCOSIDASEBeta-glucosidase | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / METAGENOME / B-GLICOSIDASE / FUNCTIONAL FOOD / PREBIOTICS / MICROBIOTA / GLUCOSE | ||||||
Function / homology | beta-D-glucopyranose Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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 | 5k6m.cif.gz | 173.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k6m.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 5k6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/5k6m ftp://data.pdbj.org/pub/pdb/validation_reports/k6/5k6m | HTTPS FTP |
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-Related structure data
Related structure data | 5k6lSC 5k6nC 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 / References: beta-glucosidase |
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#2: Sugar | ChemComp-BGC / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.72 Å3/Da / Density % sol: 54.8 % / Description: Elongated bar |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, then soaked in 20% glucose. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2014 |
Radiation | Monochromator: KB MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→95.02 Å / Num. obs: 51199 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.127 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.17→2.24 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K6L Resolution: 2.17→95.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.723 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.176 / 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: 31.178 Å2
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Refinement step | Cycle: 1 / Resolution: 2.17→95.02 Å
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Refine LS restraints |
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