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Yorodumi- PDB-7dif: GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dif | ||||||||||||
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Title | GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-angstrom resolution | ||||||||||||
Components | Non-reducing end beta-L-arabinofuranosidase | ||||||||||||
Keywords | HYDROLASE / (alpha/alpha)6 barrel / glycoside hydrolase family 127 | ||||||||||||
Function / homology | Function and homology information non-reducing end beta-L-arabinofuranosidase / beta-L-arabinofuranosidase activity / polysaccharide catabolic process / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Bifidobacterium longum subsp. longum (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||||||||
Authors | Amaki, S. / McGregor, N.G.S. / Arakawa, T. / Yamada, C. / Borlandelli, V. / Overkleeft, H.S. / Davies, G.J. / Fushinobu, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor. Authors: McGregor, N.G.S. / Coines, J. / Borlandelli, V. / Amaki, S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Yamada, C. / Arakawa, T. / Ishiwata, A. / Ito, Y. / van der Marel, G.A. / Codee, J.D.C. ...Authors: McGregor, N.G.S. / Coines, J. / Borlandelli, V. / Amaki, S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Yamada, C. / Arakawa, T. / Ishiwata, A. / Ito, Y. / van der Marel, G.A. / Codee, J.D.C. / Fushinobu, S. / Overkleeft, H.S. / Rovira, C. / Davies, G.J. #1: Journal: Biochem. Biophys. Res. Commun. / Year: 2014 Title: Crystal structure of glycoside hydrolase family 127 beta-L-arabinofuranosidase from Bifidobacterium longum. Authors: Ito, T. / Saikawa, K. / Kim, S. / Fujita, K. / Ishiwata, A. / Kaeothip, S. / Arakawa, T. / Wakagi, T. / Beckham, G.T. / Ito, Y. / Fushinobu, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dif.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dif.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dif_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7dif_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7dif_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 7dif_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/7dif ftp://data.pdbj.org/pub/pdb/validation_reports/di/7dif | HTTPS FTP |
-Related structure data
Related structure data | 6yqhC 7bzlC 3wkxS C: citing same article (ref.) S: Starting model for refinement |
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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: 74457.906 Da / Num. of mol.: 1 / Fragment: glycoside hydrolase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b) (bacteria) Strain: ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b Gene: hypBA1, BLLJ_0211 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) References: UniProt: E8MGH8, non-reducing end beta-L-arabinofuranosidase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-FE0 / ( |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES-NaOH (pH 6.5), 0.7 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 10, 2020 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.05 Å / Num. obs: 90295 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 34.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 10.1 % / Rmerge(I) obs: 3.325 / Num. unique obs: 4409 / CC1/2: 0.67 / Rpim(I) all: 1.527 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WKX Resolution: 1.75→46.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 140.17 Å2 / Biso mean: 42.661 Å2 / Biso min: 28.07 Å2
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Refinement step | Cycle: final / Resolution: 1.75→46.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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