+
Open data
-
Basic information
Entry | Database: PDB / ID: 7svi | ||||||
---|---|---|---|---|---|---|---|
Title | Bile Salt Hydrolase C from Lactobacillus johnsonii | ||||||
![]() | Choloylglycine hydrolase | ||||||
![]() | HYDROLASE / bile salt hydrolase | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walker, M.E. / Redinbo, M.R. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. Authors: Foley, M.H. / Walker, M.E. / Stewart, A.K. / O'Flaherty, S. / Gentry, E.C. / Patel, S. / Beaty, V.V. / Allen, G. / Pan, M. / Simpson, J.B. / Perkins, C. / Vanhoy, M.E. / Dougherty, M.K. / ...Authors: Foley, M.H. / Walker, M.E. / Stewart, A.K. / O'Flaherty, S. / Gentry, E.C. / Patel, S. / Beaty, V.V. / Allen, G. / Pan, M. / Simpson, J.B. / Perkins, C. / Vanhoy, M.E. / Dougherty, M.K. / McGill, S.K. / Gulati, A.S. / Dorrestein, P.C. / Baker, E.S. / Redinbo, M.R. / Barrangou, R. / Theriot, C.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 349.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 227.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451 KB | Display | |
Data in XML | ![]() | 57.9 KB | Display | |
Data in CIF | ![]() | 89.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sveC ![]() 7svfC ![]() 7svgC ![]() 7svhC ![]() 7svjC ![]() 7svkC ![]() 2hezS S: Starting model for refinement C: citing same article ( |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 35798.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | The authors have deposited the sequence for Choloylglycine hydrolase in the GenBank database. The ...The authors have deposited the sequence for Choloylglycine hydrolase in the GenBank database. The accession number is OL690427. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.78 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Citrate:HCl, pH 5.6, 10% (w/v) PEG 4000, 10% (v/v) isopropanol. Crystals formed in a 2:1 protein (10.3 mg/mL) to mother liquor ratio. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→45.29 Å / Num. obs: 263785 / % possible obs: 97.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 22.58 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.0495 / Rrim(I) all: 0.07 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 22181 / CC1/2: 0.48 / CC star: 0.805 / Rpim(I) all: 0.68 / Rrim(I) all: 0.961 / % possible all: 82.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2HEZ Resolution: 1.45→45.29 Å / SU ML: 0.2079 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.1557 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: 27.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→45.29 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|