+Open data
-Basic information
Entry | Database: PDB / ID: 7o8c | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of SGBP BO2743 from Bacteroides ovatus | |||||||||
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 / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / SusD/RagB family nutrient-binding outer membrane lipoprotein Function and homology information | |||||||||
Biological species | Bacteroides ovatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Correia, V.C. / Trovao, F. / Pinheiro, B.A. / Palma, A.S. / Carvalho, A.L. | |||||||||
Funding support | Portugal, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7o8c.cif.gz | 313.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7o8c.ent.gz | 204.8 KB | Display | PDB format |
PDBx/mmJSON format | 7o8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/7o8c ftp://data.pdbj.org/pub/pdb/validation_reports/o8/7o8c | HTTPS FTP |
---|
-Related structure data
Related structure data | 7noxC 5j5uS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 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 (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153) (bacteria) Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02743 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7LY27 |
---|
-Non-polymers , 6 types, 576 molecules
#2: Chemical | ChemComp-HED / #3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein at 13.7 mg/mL; 2.0 M Ammonium Sulphate, 0.1 M BIS-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2→55.56 Å / Num. obs: 123741 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 29.4 Å2 / CC1/2: 0.845 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 9068 / CC1/2: 0.338 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J5U Resolution: 2→55.56 Å / SU ML: 0.2325 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 23.0006 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→55.56 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|