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Yorodumi- PDB-8etf: Bile Salt Hydrolase B from Lactobacillus gasseri with covalent in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8etf | ||||||
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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: 1.79 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 | 8etf.cif.gz | 576.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8etf.ent.gz | 431.7 KB | Display | PDB format |
PDBx/mmJSON format | 8etf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8etf_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8etf_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8etf_validation.xml.gz | 101.3 KB | Display | |
Data in CIF | 8etf_validation.cif.gz | 143.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/8etf ftp://data.pdbj.org/pub/pdb/validation_reports/et/8etf | HTTPS FTP |
-Related structure data
Related structure data | 8esgC 8esiC 8eslC 8eteC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37132.645 Da / Num. of mol.: 8 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 | ChemComp-WU5 / ( #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: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M proline, 0.1M HEPES:NaOH, pH 7.5, 10% (w/v) PEG 3350. Crystals grew in a 2:1 protein:crystallant ratio at a 11.4 mg/mL final protein concentration. Inhibitor was incubated with protein prior to tray setup. |
-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: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→45.86 Å / Num. obs: 296253 / % possible obs: 99.51 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.47 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1344 / Rpim(I) all: 0.06826 / Rrim(I) all: 0.1344 / Net I/σ(I): 6.43 |
Reflection shell | Resolution: 1.79→1.854 Å / Redundancy: 3.8 % / Rmerge(I) obs: 2.275 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 29558 / CC1/2: 0.195 / CC star: 0.572 / Rpim(I) all: 1.331 / Rrim(I) all: 2.645 / % possible all: 97.73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7SVH Resolution: 1.79→45.86 Å / SU ML: 0.2688 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3673 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: 38.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→45.86 Å
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Refine LS restraints |
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LS refinement shell |
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