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- PDB-7svj: Bile Salt Hydrolase from Lactobacillus ingluviei -

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Basic information

Entry
Database: PDB / ID: 7svj
TitleBile Salt Hydrolase from Lactobacillus ingluviei
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / bile salt hydrolase
Function / homologyCholoylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / hydrolase activity / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Choloylglycine hydrolase
Function and homology information
Biological speciesLactobacillus ingluviei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsWalker, M.E. / Patel, S. / 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: Nat Microbiol / Year: 2023
Title: Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut.
Authors: Foley, M.H. / Walker, M.E. / Stewart, A.K. / O'Flaherty, S. / Gentry, E.C. / Patel, S. / Beaty, V.V. / Allen, G. / Pan, M. / Simpson, J.B. / Perkins, C. / Vanhoy, M.E. / Dougherty, M.K. / ...Authors: Foley, M.H. / Walker, M.E. / Stewart, A.K. / O'Flaherty, S. / Gentry, E.C. / Patel, S. / Beaty, V.V. / Allen, G. / Pan, M. / Simpson, J.B. / Perkins, C. / Vanhoy, M.E. / Dougherty, M.K. / McGill, S.K. / Gulati, A.S. / Dorrestein, P.C. / Baker, E.S. / Redinbo, M.R. / Barrangou, R. / Theriot, C.M.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9579
Polymers75,0372
Non-polymers9197
Water8,593477
1
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,91318
Polymers150,0754
Non-polymers1,83814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area23500 Å2
ΔGint-51 kcal/mol
Surface area42770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.636, 43.810, 155.060
Angle α, β, γ (deg.)90.000, 99.360, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Choloylglycine hydrolase /


Mass: 37518.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus ingluviei (bacteria) / Gene: FC43_GL000624 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R1U3N2

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Non-polymers , 5 types, 484 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium Acetate Hydrate, 0.1M Tris:HCl pH 7.0, 20% (w/v) PEG 3000. Crystals formed in a 1:2 protein (13.8 mg/mL) to mother liquor ratio.

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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 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→42.12 Å / Num. obs: 108742 / % possible obs: 97.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.75 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Rrim(I) all: 0.057 / Net I/σ(I): 8.5
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 10677 / CC1/2: 0.413 / CC star: 0.765 / Rpim(I) all: 0.9788 / Rrim(I) all: 1.384 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HEZ

2hez


Resolution: 1.43→42.12 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203 1999 -
Rwork0.1774 --
obs-108659 97.4 %
Displacement parametersBiso mean: 24.32 Å2
Refinement stepCycle: LAST / Resolution: 1.43→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 58 477 5667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055322
X-RAY DIFFRACTIONf_angle_d0.82087253
X-RAY DIFFRACTIONf_chiral_restr0.0817801
X-RAY DIFFRACTIONf_plane_restr0.0049953
X-RAY DIFFRACTIONf_dihedral_angle_d15.86441882
LS refinement shellResolution: 1.43→1.48 Å
RfactorNum. reflection% reflection
Rfree0.3664 196 -
Rwork0.3623 10646 -
obs--95.9 %

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