+Open data
-Basic information
Entry | Database: PDB / ID: 7kv4 | ||||||
---|---|---|---|---|---|---|---|
Title | Surface glycan-binding protein A from Bacteroides fluxus | ||||||
Components | SusD family protein | ||||||
Keywords | SUGAR BINDING PROTEIN / SusD / Tetratricopeptide repeat / CBM | ||||||
Function / homology | SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / cell outer membrane / Tetratricopeptide-like helical domain superfamily / SusD family protein Function and homology information | ||||||
Biological species | Bacteroides fluxus YIT 12057 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å | ||||||
Authors | Tamura, K. / Brumer, H. / Van Petegem, F. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota. Authors: Tamura, K. / Dejean, G. / Van Petegem, F. / Brumer, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7kv4.cif.gz | 180 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7kv4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7kv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/7kv4 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kv4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7kv1C 7kv2C 7kv3C 7kv5C 7kv6C 7kv7C 7kwbC 7kwcC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 57254.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fluxus YIT 12057 (bacteria) Gene: HMPREF9446_00614 / Production host: Escherichia coli (E. coli) / References: UniProt: F3PPH4 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 0.1 M tris pH8.1, 0.2 M magnesium chloride, 23 % (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→36.431 Å / Num. obs: 45565 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.987 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.84→1.88 Å / Num. unique obs: 2369 / CC1/2: 0.793 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.84→36.431 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.292 / WRfactor Rwork: 0.246 / Average fsc free: 0.8811 / Average fsc work: 0.902 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.135 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.088 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→36.431 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|