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Yorodumi- PDB-8esg: Bile Salt Hydrolase B from Lactobacillus gasseri with covalent in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8esg | ||||||
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Title | Bile Salt Hydrolase B from Lactobacillus gasseri with covalent inhibitor bound | ||||||
Components | Choloylglycine hydrolase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / bile salt hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus gasseri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Walker, M.E. / Redinbo, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structural diversity of bile salt hydrolases reveals rationale for substrate selectivity Authors: Walker, M.E. / Redinbo, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8esg.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8esg.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 8esg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8esg_validation.pdf.gz | 968.9 KB | Display | wwPDB validaton report |
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Full document | 8esg_full_validation.pdf.gz | 974 KB | Display | |
Data in XML | 8esg_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 8esg_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/8esg ftp://data.pdbj.org/pub/pdb/validation_reports/es/8esg | HTTPS FTP |
-Related structure data
Related structure data | 8esiC 8eslC 8eteC 8etfC 8etkC 8ewtC 8faoC 7svhS 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: 37132.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus gasseri (bacteria) / Gene: F8244_03005 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A833FHE1 #2: Chemical | 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: 3.39 Å3/Da / Density % sol: 63.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH, pH 10.5, 2M Ammonium Sulfate. Crystals formed in a 2:1 ratio of protein:mother liquor. 2.5 uM protein was incubated with 50 uM inhibitor for 1h at ...Details: 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH, pH 10.5, 2M Ammonium Sulfate. Crystals formed in a 2:1 ratio of protein:mother liquor. 2.5 uM protein was incubated with 50 uM inhibitor for 1h at 37oC. Mixture was washed 3x with buffer in a spin concentrator and then concentrated to 8 mg/mL final concentration. |
-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: 1.03 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→48.95 Å / Num. obs: 100941 / % possible obs: 99.8 % / Redundancy: 20.8 % / Biso Wilson estimate: 63.96 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.028 / Rrim(I) all: 0.128 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.18→2.258 Å / Redundancy: 21.7 % / Rmerge(I) obs: 6.367 / Mean I/σ(I) obs: 0.57 / Num. unique obs: 5296 / CC1/2: 0.209 / CC star: 0.588 / Rpim(I) all: 1.38 / Rrim(I) all: 6.518 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7SVH Resolution: 2.18→48.95 Å / SU ML: 0.4593 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.6343 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→48.95 Å
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Refine LS restraints |
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LS refinement shell |
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