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- PDB-7svf: Bile salt hydrolase A from Lactobacillus gasseri with taurine bound -

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Basic information

Entry
Database: PDB / ID: 7svf
TitleBile salt hydrolase A from Lactobacillus gasseri with taurine bound
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / bile salt hydrolase
Function / homologyPenicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / 4-Layer Sandwich / Alpha Beta / : / 2-AMINOETHANESULFONIC ACID / :
Function and homology information
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)144,02010
Polymers143,4414
Non-polymers5796
Water16,862936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Oligomeric state is evident from crystal structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.323, 153.548, 94.098
Angle α, β, γ (deg.)90.000, 105.810, 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
Choloylglycine hydrolase


Mass: 35860.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus gasseri (bacteria) / Gene: bsh, J3E66_000057 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8A6B131, choloylglycine hydrolase
#2: Chemical
ChemComp-TAU / 2-AMINOETHANESULFONIC ACID


Mass: 125.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H7NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 936 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium Sulfate, 20% (w/v) PEG 3350. Crystals formed in a 1:2 protein (9.55 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-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→45 Å / Num. obs: 100601 / % possible obs: 99.4 % / Redundancy: 1.9 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.096 / Net I/σ(I): 6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9994 / CC1/2: 0.81 / CC star: 0.946 / Rpim(I) all: 0.2958 / Rrim(I) all: 0.418 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HEZ

2hez


Resolution: 2.05→45 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1959 --
Rwork0.1607 --
obs-100601 99.4 %
Displacement parametersBiso mean: 24.73 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 30 936 10722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006910024
X-RAY DIFFRACTIONf_angle_d0.792613649
X-RAY DIFFRACTIONf_chiral_restr0.05411504
X-RAY DIFFRACTIONf_plane_restr0.00461757
X-RAY DIFFRACTIONf_dihedral_angle_d14.67693507

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