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Yorodumi- PDB-7nox: Structure of SGBP BO2743 from Bacteroides ovatus in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nox | |||||||||
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Title | Structure of SGBP BO2743 from Bacteroides ovatus in complex with mixed-linked gluco-nonasaccharide | |||||||||
Components | Surface glycan-binding protein BO2743 | |||||||||
Keywords | SUGAR BINDING PROTEIN / Bacteroides ovatus / surface glycan binding protein (SGBP) / SusD-homologue / Polysaccharide Utilization Loci (PUL) / gut microbiota / beta-glucans / barley-9 | |||||||||
Function / homology | SusD-like 2 / Starch-binding associating with outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / AZIDE ION / TRIETHYLENE GLYCOL / SusD/RagB family nutrient-binding outer membrane lipoprotein Function and homology information | |||||||||
Biological species | Bacteroides ovatus ATCC 8483 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | |||||||||
Authors | Correia, V.C. / Trovao, F. / Pinheiro, B.A. / Palma, A.S. / Carvalho, A.L. | |||||||||
Funding support | Portugal, 2items
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Citation | Journal: Microbiol Spectr / Year: 2021 Title: Mapping Molecular Recognition of beta 1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus. Authors: Correia, V.G. / Trovao, F. / Pinheiro, B.A. / Bras, J.L.A. / Silva, L.M. / Nunes, C. / Coimbra, M.A. / Liu, Y. / Feizi, T. / Fontes, C.M.G.A. / Mulloy, B. / Chai, W. / Carvalho, A.L. / Palma, A.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nox.cif.gz | 254.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nox.ent.gz | 199.4 KB | Display | PDB format |
PDBx/mmJSON format | 7nox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nox_validation.pdf.gz | 941 KB | Display | wwPDB validaton report |
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Full document | 7nox_full_validation.pdf.gz | 946.2 KB | Display | |
Data in XML | 7nox_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 7nox_validation.cif.gz | 72.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/7nox ftp://data.pdbj.org/pub/pdb/validation_reports/no/7nox | HTTPS FTP |
-Related structure data
Related structure data | 7o8cC 5j5uS 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
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 67918.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria) Gene: BACOVA_02743 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7LY27 #2: Polysaccharide | Type: oligosaccharide / Mass: 1477.282 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source |
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-Non-polymers , 7 types, 1023 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PGE / #6: Chemical | #7: Chemical | ChemComp-AZI / #8: Chemical | ChemComp-TAM / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein at 8 mg/mL; 25% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 mM MgCl2.6H2O |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→62.32 Å / Num. obs: 175289 / % possible obs: 96.5 % / Redundancy: 9 % / CC1/2: 1 / Net I/σ(I): 1.6 |
Reflection shell | Resolution: 1.43→1.55 Å / Num. unique obs: 8764 / CC1/2: 0.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J5U Resolution: 1.43→44.86 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 80.83 Å2 / Biso mean: 23.0947 Å2 / Biso min: 10.51 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→44.86 Å
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LS refinement shell | Resolution: 1.43→1.45 Å
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