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- PDB-8ete: Bile Salt Hydrolase from B. longum with covalent inhibitor bound -

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Basic information

Entry
Database: PDB / ID: 8ete
TitleBile Salt Hydrolase from B. longum with covalent inhibitor bound
ComponentsConjugated bile acid hydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / bile salt hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chenodeoxycholoyltaurine hydrolase / chenodeoxycholoyltaurine hydrolase activity / choloylglycine hydrolase activity / choloylglycine hydrolase / bile acid biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / transferase activity
Similarity search - Function
: / : / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Chem-WU5 / Bile salt hydrolase/transferase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWalker, M.E. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135218 United States
CitationJournal: To Be Published
Title: Structural diversity of bile salt hydrolases reveals rationale for substrate selectivity
Authors: Walker, M.E. / Redinbo, M.R.
History
DepositionOct 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conjugated bile acid hydrolase
B: Conjugated bile acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1574
Polymers70,3722
Non-polymers7852
Water00
1
A: Conjugated bile acid hydrolase
B: Conjugated bile acid hydrolase
hetero molecules

A: Conjugated bile acid hydrolase
B: Conjugated bile acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3148
Polymers140,7444
Non-polymers1,5704
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area14790 Å2
ΔGint-101 kcal/mol
Surface area41200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.085, 100.085, 165.187
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Conjugated bile acid hydrolase / Bile salt hydrolase / BSH / Chenodeoxycholoyltaurine hydrolase / Choloylglycine hydrolase


Mass: 35185.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: bsh / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KK62, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, chenodeoxycholoyltaurine hydrolase, choloylglycine hydrolase
#2: Chemical ChemComp-WU5 / (5R)-1-fluoro-5-[(1R,3aS,3bR,5aR,7R,9aS,9bS,11aR)-7-hydroxy-9a,11a-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-1-yl]hexan-2-one (non-preferred name)


Mass: 392.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H41FO2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG4000, 0.2 M lithium sulfate. Protein crystallized in a 1:2 protein:crystallant ratio. Protein was incubated with inhibitor prior ...Details: 0.1 M sodium acetate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG4000, 0.2 M lithium sulfate. Protein crystallized in a 1:2 protein:crystallant ratio. Protein was incubated with inhibitor prior to tray setup and was 8.55 mg/mL final concentration.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→47.89 Å / Num. obs: 43164 / % possible obs: 97.78 % / Redundancy: 10.4 % / Biso Wilson estimate: 60.28 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.3254 / Rpim(I) all: 0.1054 / Rrim(I) all: 0.3424 / Net I/σ(I): 7.05
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 10.2 % / Num. unique obs: 4255 / CC1/2: 0.122 / % possible all: 83.71

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HF0

2hf0


Resolution: 2.3→47.89 Å / SU ML: 0.5279 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.9176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2838 2015 4.77 %
Rwork0.2508 40240 -
obs0.2531 42255 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.93 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 54 0 4782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284916
X-RAY DIFFRACTIONf_angle_d0.54956714
X-RAY DIFFRACTIONf_chiral_restr0.0441732
X-RAY DIFFRACTIONf_plane_restr0.0033874
X-RAY DIFFRACTIONf_dihedral_angle_d5.9476724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.57891200.51062405X-RAY DIFFRACTION83.72
2.36-2.420.52971360.48262604X-RAY DIFFRACTION89.66
2.42-2.490.42581390.44462818X-RAY DIFFRACTION97.4
2.49-2.570.4481480.41882894X-RAY DIFFRACTION99.38
2.57-2.660.36911470.40562896X-RAY DIFFRACTION99.77
2.67-2.770.4311420.38932882X-RAY DIFFRACTION99.97
2.77-2.90.42791470.35922911X-RAY DIFFRACTION99.61
2.9-3.050.32831430.32352931X-RAY DIFFRACTION99.93
3.05-3.240.33731500.30492926X-RAY DIFFRACTION99.97
3.24-3.490.30651450.27162916X-RAY DIFFRACTION99.74
3.49-3.840.28521470.23832956X-RAY DIFFRACTION99.65
3.84-4.40.23731450.21062973X-RAY DIFFRACTION100
4.4-5.540.20471490.1842996X-RAY DIFFRACTION99.97
5.54-47.890.22711570.18613132X-RAY DIFFRACTION100

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