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- PDB-7sve: Bile Salt Hydrolase A from Lactobacillus acidophilus -

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Basic information

Entry
Database: PDB / ID: 7sve
TitleBile Salt Hydrolase A from Lactobacillus acidophilus
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / bile salt hydrolase
Function / homology
Function and homology information


choloylglycine hydrolase activity / choloylglycine hydrolase
Similarity search - Function
: / : / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
choloylglycine hydrolase
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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


Theoretical massNumber of molelcules
Total (without water)151,7894
Polymers151,7894
Non-polymers00
Water14,448802
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Tetramer is evident in crystal structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17780 Å2
ΔGint-65 kcal/mol
Surface area44780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.561, 92.953, 87.057
Angle α, β, γ (deg.)90.000, 107.220, 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: 37947.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: bshA, CXB72_06680 / Production host: Escherichia coli (E. coli) / References: UniProt: G1U9U5, choloylglycine hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M DL-Malic Acid, pH 7.0, 20% (w/v) PEG 3350. Crystals formed in a 2:1 protein (11.6 mg/mL):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: 2.15→46.48 Å / Num. obs: 68775 / % possible obs: 98.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 29.63 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.0548 / Rrim(I) all: 0.078 / Net I/σ(I): 10.5
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6798 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.3231 / Rrim(I) all: 0.457 / % possible all: 97.4

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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: 2.15→46.48 Å / SU ML: 0.1991 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 19.7861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2051 2001 2.91 %
Rwork0.1511 66765 -
obs0.1527 68766 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.94 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10343 0 0 802 11145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007110632
X-RAY DIFFRACTIONf_angle_d0.884614412
X-RAY DIFFRACTIONf_chiral_restr0.05491538
X-RAY DIFFRACTIONf_plane_restr0.00491901
X-RAY DIFFRACTIONf_dihedral_angle_d8.4251405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.26361350.20214720X-RAY DIFFRACTION97.43
2.2-2.260.23151460.18194711X-RAY DIFFRACTION97.65
2.26-2.330.23741380.17364742X-RAY DIFFRACTION97.74
2.33-2.410.21611460.1724715X-RAY DIFFRACTION97.85
2.41-2.490.23881390.17484760X-RAY DIFFRACTION97.88
2.49-2.590.24821430.1644713X-RAY DIFFRACTION98.28
2.59-2.710.22291480.16394774X-RAY DIFFRACTION98.09
2.71-2.850.22281450.16194744X-RAY DIFFRACTION98.25
2.85-3.030.24281430.16474800X-RAY DIFFRACTION98.33
3.03-3.260.22671400.15874771X-RAY DIFFRACTION98.38
3.26-3.590.21091370.14534761X-RAY DIFFRACTION98.02
3.59-4.110.17531450.12714802X-RAY DIFFRACTION98.51
4.11-5.180.16111420.11864849X-RAY DIFFRACTION99.09
5.18-46.480.18131540.15714903X-RAY DIFFRACTION98.65

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