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Yorodumi- PDB-7exw: GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7exw | ||||||||||||
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Title | GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with alpha-L-arabinofuranosylamide | ||||||||||||
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 / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||||||||
Authors | Sawano, K. / Arakawa, T. / Yamada, C. / Fujita, K. / Fushinobu, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Glycobiology / Year: 2022 Title: Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase. Authors: Maruyama, S. / Sawano, K. / Amaki, S. / Suzuki, T. / Narita, S. / Kimura, K. / Arakawa, T. / Yamada, C. / Ito, Y. / Dohmae, N. / Fujita, K. / Ishiwata, A. / Fushinobu, S. #1: Journal: Biochemical and Biophysical Research Communications 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. / Wkagi, 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 | 7exw.cif.gz | 145.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7exw.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 7exw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7exw_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7exw_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7exw_validation.xml.gz | 25 KB | Display | |
Data in CIF | 7exw_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/7exw ftp://data.pdbj.org/pub/pdb/validation_reports/ex/7exw | HTTPS FTP |
-Related structure data
Related structure data | 7exuC 7exvC 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: pET23 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 References: UniProt: E8MGH8, non-reducing end beta-L-arabinofuranosidase |
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#2: Sugar | ChemComp-09X / |
#3: Chemical | ChemComp-ZN / |
#4: 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: 2.73 Å3/Da / Density % sol: 54.95 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.7 M sodium citrate, 0.1 M MES-NaOH (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2019 |
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: 2.2→45.2 Å / Num. obs: 42003 / % possible obs: 98.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 37.54 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.066 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2055 / CC1/2: 0.816 / Rpim(I) all: 0.309 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3WKX Resolution: 2.2→45.2 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.114 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.22 / 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: 148.7 Å2 / Biso mean: 49.049 Å2 / Biso min: 33.93 Å2
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Refinement step | Cycle: final / Resolution: 2.2→45.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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