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Yorodumi- PDB-5gqg: Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gqg | |||||||||
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Title | Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, galacto-N-biose complex | |||||||||
Components | Lacto-N-biosidase | |||||||||
Keywords | HYDROLASE / beta-helix | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bifidobacterium longum subsp. longum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | |||||||||
Authors | Yamada, C. / Arakawa, T. / Katayama, T. / Fushinobu, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Cell Chem Biol / Year: 2017 Title: Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum Authors: Yamada, C. / Gotoh, A. / Sakanaka, M. / Hattie, M. / Stubbs, K.A. / Katayama-Ikegami, A. / Hirose, J. / Kurihara, S. / Arakawa, T. / Kitaoka, M. / Okuda, S. / Katayama, T. / Fushinobu, S. #1: Journal: J. Biol. Chem. / Year: 2013 Title: Lacto-N-biosidase encoded by a novel gene of Bifidobacterium longum subspecies longum shows unique substrate specificity and requires a designated chaperone for its active expression. Authors: Sakurama, H. / Kiyohara, M. / Wada, J. / Honda, Y. / Yamaguchi, M. / Fukiya, S. / Yokota, A. / Ashida, H. / Kumagai, H. / Kitaoka, M. / Yamamoto, K. / Katayama, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gqg.cif.gz | 239.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gqg.ent.gz | 189 KB | Display | PDB format |
PDBx/mmJSON format | 5gqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gqg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5gqg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5gqg_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 5gqg_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/5gqg ftp://data.pdbj.org/pub/pdb/validation_reports/gq/5gqg | HTTPS FTP |
-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: 66090.375 Da / Num. of mol.: 2 / Fragment: UNP residues 31-625 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. longum (bacteria) Strain: JCM1217 / Gene: lnbX / Plasmid: pTK2385 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): delta-lacZ (DE3)/pRARE2 / References: UniProt: A0A024QYS6, lacto-N-biosidase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: 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: 2.6 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M ammonium fluoride, 0.1 M MES-NaOH, 20-21% (v/v) PEG3350, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2015 |
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: 2.7→102 Å / Num. obs: 37608 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.88 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→102 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 15.966 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.35 / 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: 50.162 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→102 Å
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Refine LS restraints |
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