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Yorodumi- PDB-5wzr: Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wzr | |||||||||
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Title | Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex | |||||||||
Components | Alpha-N-acetylgalactosaminidase | |||||||||
Keywords | HYDROLASE / Glycoside Hydrolase | |||||||||
Function / homology | Protein of unknown function DUF5696 / Family of unknown function (DUF5696) / Endo-alpha-N-acetylgalactosaminidase / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / Chem-DJN / Alpha-N-acetylgalactosaminidase Function and homology information | |||||||||
Biological species | Bifidobacterium bifidum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å | |||||||||
Authors | Sato, M. / Arakawa, T. / Ashida, H. / Fushinobu, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors Authors: Sato, M. / Liebschner, D. / Yamada, Y. / Matsugaki, N. / Arakawa, T. / Wills, S.S. / Hattie, M. / Stubbs, K.A. / Ito, T. / Senda, T. / Ashida, H. / Fushinobu, S. #1: Journal: J. Biol. Chem. / Year: 2012 Title: alpha-N-acetylgalactosaminidase from infant-associated bifidobacteria belonging to novel glycoside hydrolase family 129 is implicated in alternative mucin degradation pathway Authors: Kiyohara, M. / Nakatomi, T. / Kurihara, S. / Fushinobu, S. / Suzuki, H. / Tanaka, T. / Shoda, S. / Kitaoka, M. / Katayama, T. / Yamamoto, K. / Ashida, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wzr.cif.gz | 258.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wzr.ent.gz | 207.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/5wzr ftp://data.pdbj.org/pub/pdb/validation_reports/wz/5wzr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 72232.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Strain: JCM 1254 Gene: nagBb, A0008_0340, APS66_09030, LMG11582_0481, LMG11583_0397 Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CodonPlus-RIL References: UniProt: G5ELM1, alpha-N-acetylgalactosaminidase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.02M MgCl2, 0.1M HEPES-NaOH, 7.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 5, 2016 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→103.95 Å / Num. obs: 37110 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.79→2.85 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.979 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.79→103.95 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.864 / SU B: 24.947 / SU ML: 0.459 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / 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: 79.962 Å2
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Refinement step | Cycle: 1 / Resolution: 2.79→103.95 Å
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Refine LS restraints |
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