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Yorodumi- PDB-6r4k: Structure of beta-glucosidase A from Paenibacillus polymyxa compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r4k | ||||||
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Title | Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with a monovalent inhibitor | ||||||
Components | Beta-glucosidase A | ||||||
Keywords | HYDROLASE / BETA-GLUCOSIDASE / GLYCOSIDASE / CARBOHYDRATE / CARBOHYDRATE METABOLISM / POLISACCHARIDE DEGRADATION / COMPLEX / INHIBITOR | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | ||||||
Biological species | Paenibacillus polymyxa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Jimenez-Ortega, E. / Sanz-Aparicio, J. | ||||||
Citation | Journal: Bioorg.Chem. / Year: 2019 Title: Structural basis of the inhibition of GH1 beta-glucosidases by multivalent pyrrolidine iminosugars. Authors: Martinez-Bailen, M. / Jimenez-Ortega, E. / Carmona, A.T. / Robina, I. / Sanz-Aparicio, J. / Talens-Perales, D. / Polaina, J. / Matassini, C. / Cardona, F. / Moreno-Vargas, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r4k.cif.gz | 383.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r4k.ent.gz | 317.1 KB | Display | PDB format |
PDBx/mmJSON format | 6r4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/6r4k ftp://data.pdbj.org/pub/pdb/validation_reports/r4/6r4k | HTTPS FTP |
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-Related structure data
Related structure data | 6qwiC 1e4iS 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: 51608.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus polymyxa (bacteria) / Gene: bglA / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / References: UniProt: P22073, beta-glucosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.31 % / Description: Prismatic crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 18% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD), 0.1 M Bis-Tris propane, pH 7.5, and 5% n-Dodecyl beta-D-maltoside. Cryoprotectant mother liquor supplemented with 25% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 22, 2018 / Details: KB focusing mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→48.91 Å / Num. obs: 85545 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.13→2.17 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4461 / CC1/2: 0.655 / Rpim(I) all: 0.299 / Rrim(I) all: 0.765 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1E4I Resolution: 2.13→48.646 Å / Cross valid method: FREE R-VALUE / σ(F): 83 / Phase error: 28.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→48.646 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.8397 Å / Origin y: -39.7753 Å / Origin z: 45.1114 Å
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Refinement TLS group | Selection details: all |