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Yorodumi- PDB-7svg: Bile Salt Hydrolase A from Lactobacillus gasseri with chenodeoxyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7svg | ||||||
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Title | Bile Salt Hydrolase A from Lactobacillus gasseri with chenodeoxycholate and taurine bound | ||||||
Components | Choloylglycine hydrolase | ||||||
Keywords | HYDROLASE / bile salt hydrolase | ||||||
Function / homology | CHENODEOXYCHOLIC ACID / 2-AMINOETHANESULFONIC ACID / : Function and homology information | ||||||
Biological species | Lactobacillus gasseri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Walker, M.E. / Redinbo, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Microbiol / Year: 2023 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7svg.cif.gz | 355.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7svg.ent.gz | 229.3 KB | Display | PDB format |
PDBx/mmJSON format | 7svg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7svg_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7svg_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7svg_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 7svg_validation.cif.gz | 90.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/7svg ftp://data.pdbj.org/pub/pdb/validation_reports/sv/7svg | HTTPS FTP |
-Related structure data
Related structure data | 7sveC 7svfC 7svhC 7sviC 7svjC 7svkC 2hezS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35908.262 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus gasseri (bacteria) / Gene: bsh, J3E66_000057 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8A6B131, choloylglycine hydrolase #2: Chemical | ChemComp-TAU / #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.88 Å3/Da / Density % sol: 57.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3 streak seeded with crystals grown in 20% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3. Crystals were grown in a protein (9.55 mg/mL):mother ...Details: 18% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3 streak seeded with crystals grown in 20% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3. Crystals were grown in a protein (9.55 mg/mL):mother liquor ratio of 1:2. Crystal seeds were streaked into this condition from a broad screen hit and then the resultant crystals were soaked in 1:1 ratio of mother liquor:100 mM TCDCA for 24h before looping. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→29.34 Å / Num. obs: 332715 / % possible obs: 92.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.08 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.09959 / Rpim(I) all: 0.05829 / Rrim(I) all: 0.1158 / Net I/σ(I): 6.16 |
Reflection shell | Resolution: 1.352→1.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.518 / Mean I/σ(I) obs: 0.44 / Num. unique obs: 29313 / CC1/2: 0.317 / CC star: 0.694 / Rpim(I) all: 0.9715 / Rrim(I) all: 1.814 / % possible all: 72.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HEZ Resolution: 1.35→29.34 Å / SU ML: 0.2517 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8431 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→29.34 Å
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Refine LS restraints |
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LS refinement shell |
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