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

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Basic information

Entry
Database: PDB / ID: 8esi
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-WSR / Bile salt hydrolase/transferase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWalker, M.E. / Lim, L. / 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. / Lim, L. / Redinbo, M.R.
History
DepositionOct 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Conjugated bile acid hydrolase
B: Conjugated bile acid hydrolase
C: Conjugated bile acid hydrolase
D: Conjugated bile acid hydrolase
E: Conjugated bile acid hydrolase
F: Conjugated bile acid hydrolase
G: Conjugated bile acid hydrolase
H: Conjugated bile acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,26916
Polymers281,4888
Non-polymers3,7818
Water2,450136
1
A: Conjugated bile acid hydrolase
B: Conjugated bile acid hydrolase
C: Conjugated bile acid hydrolase
D: Conjugated bile acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,6358
Polymers140,7444
Non-polymers1,8914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Conjugated bile acid hydrolase
F: Conjugated bile acid hydrolase
G: Conjugated bile acid hydrolase
H: Conjugated bile acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,6358
Polymers140,7444
Non-polymers1,8914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.072, 166.801, 103.077
Angle α, β, γ (deg.)90.000, 116.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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.: 8
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-WSR / (1R,3aS,3bR,5aR,7R,9aS,9bS,11aR)-1-[(2R)-6-fluoro-5-oxohexan-2-yl]-9a,11a-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-7-yl hydrogen sulfate (non-preferred name)


Mass: 472.653 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C25H41FO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M Tris:HCl pH 8.5, 16% (w/v) PEG 4000. Crystals formed in 1:2 ratio of protein (11.8 mg/mL) to mother liquor. 2.5 uM protein was incubated with 50 uM inhibitor for 1h at ...Details: 0.2 M MgCl2, 0.1 M Tris:HCl pH 8.5, 16% (w/v) PEG 4000. Crystals formed in 1:2 ratio of protein (11.8 mg/mL) to 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 11.8 mg/mL final concentration.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→49.1 Å / Num. obs: 116293 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 47.52 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.1771 / Rpim(I) all: 0.1076 / Rrim(I) all: 0.208 / Net I/σ(I): 5.4
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.889 / Mean I/σ(I) obs: 0.88 / Num. unique obs: 11592 / CC1/2: 0.341 / CC star: 0.713 / Rpim(I) all: 1.112 / Rrim(I) all: 2.199 / % possible all: 99.6

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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: 2.35→49.1 Å / SU ML: 0.3797 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4559
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2436 1996 1.72 %
Rwork0.2097 114143 -
obs0.2103 116139 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.03 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19151 0 248 136 19535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002219943
X-RAY DIFFRACTIONf_angle_d0.527252
X-RAY DIFFRACTIONf_chiral_restr0.04242952
X-RAY DIFFRACTIONf_plane_restr0.00313565
X-RAY DIFFRACTIONf_dihedral_angle_d15.34876894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.37921390.37758132X-RAY DIFFRACTION99.53
2.41-2.470.38631440.33878091X-RAY DIFFRACTION99.7
2.47-2.550.3341430.31868178X-RAY DIFFRACTION99.64
2.55-2.630.35931400.29298124X-RAY DIFFRACTION99.69
2.63-2.720.32491410.28258170X-RAY DIFFRACTION99.56
2.72-2.830.30061410.28958112X-RAY DIFFRACTION99.72
2.83-2.960.31951460.26528144X-RAY DIFFRACTION99.7
2.96-3.120.27841410.23738184X-RAY DIFFRACTION99.66
3.12-3.310.25651410.22248095X-RAY DIFFRACTION99.16
3.31-3.570.25761450.21228143X-RAY DIFFRACTION99.09
3.57-3.930.18921450.18818143X-RAY DIFFRACTION99.66
3.93-4.490.21351430.16268173X-RAY DIFFRACTION99.72
4.49-5.660.17671450.15618167X-RAY DIFFRACTION99.39
5.66-49.10.2141420.16698287X-RAY DIFFRACTION99.6

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