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- PDB-8ewt: Bile salt hydrolase A from Lactobacillus gasseri bound to covalen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ewt | ||||||
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Title | Bile salt hydrolase A from Lactobacillus gasseri bound to covalent probe | ||||||
![]() | Conjugated bile salt hydrolase | ||||||
![]() | HYDROLASE / bile salt hydrolase | ||||||
Function / homology | : / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / hydrolase activity / Chem-X3I / Conjugated bile salt hydrolase related amidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walker, M.E. / Redinbo, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.1 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 944.9 KB | Display | ![]() |
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Full document | ![]() | 945.7 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8esgC ![]() 8esiC ![]() 8eslC ![]() 8eteC ![]() 8etfC ![]() 8etkC ![]() 8faoC ![]() 7svfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35860.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% (w/v) PEG 4000, 20% (v/v) isopropanol. Protein was incubated with probe and then concentrated to 7.08 mg/mL. Protein crystallized in a 1:2 protein:crystallant ratio. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→48.22 Å / Num. obs: 62279 / % possible obs: 96.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.42 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.2126 / Rpim(I) all: 0.0838 / Rrim(I) all: 0.2302 / Net I/σ(I): 6.08 |
Reflection shell | Resolution: 2.03→2.103 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.811 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5470 / CC1/2: 0.146 / Rpim(I) all: 0.9079 / Rrim(I) all: 2.044 / % possible all: 88.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7SVF Resolution: 2.03→48.22 Å / SU ML: 0.2565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5591 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: 43.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→48.22 Å
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Refine LS restraints |
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LS refinement shell |
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