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- PDB-7svh: Bile Salt Hydrolase B from Lactobacillus gasseri -

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Basic information

Entry
Database: PDB / ID: 7svh
TitleBile Salt Hydrolase B from Lactobacillus gasseri
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / bile salt hydrolase
Function / homologycholoylglycine hydrolase / : / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / hydrolase activity / Choloylglycine hydrolase
Function and homology information
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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

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Assembly

Deposited unit
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
C: Choloylglycine hydrolase
D: Choloylglycine hydrolase
E: Choloylglycine hydrolase
F: Choloylglycine hydrolase
G: Choloylglycine hydrolase
H: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,15812
Polymers297,0618
Non-polymers974
Water35,4901970
1
A: Choloylglycine hydrolase
D: Choloylglycine hydrolase
hetero molecules

C: Choloylglycine hydrolase
E: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5796
Polymers148,5314
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area18760 Å2
ΔGint-100 kcal/mol
Surface area43720 Å2
MethodPISA
2
B: Choloylglycine hydrolase
F: Choloylglycine hydrolase
G: Choloylglycine hydrolase
H: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,5796
Polymers148,5314
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18660 Å2
ΔGint-99 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.350, 167.376, 88.153
Angle α, β, γ (deg.)90.000, 98.978, 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: 37132.645 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus gasseri (bacteria) / Gene: F8244_03005 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A833FHE1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1970 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M Sodium Cacodyolate:HCl, pH 6.5, 20% (w/v) PEG 1000. Crystals formed in a 1:2 ratio of protein (10.75 mg/mL) to mother liquor.

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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: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→29.02 Å / Num. obs: 348378 / % possible obs: 97.1 % / Redundancy: 2 % / Biso Wilson estimate: 24.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05921 / Rpim(I) all: 0.05921 / Rrim(I) all: 0.08373 / Net I/σ(I): 6.4
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.945 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 33984 / CC1/2: 0.194 / CC star: 0.57 / Rpim(I) all: 1.945 / Rrim(I) all: 2.75 / % possible all: 85

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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: 1.56→29.02 Å / SU ML: 0.3219 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.1602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2597 1955 0.57 %
Rwork0.2208 341374 -
obs0.221 343329 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.92 Å2
Refinement stepCycle: LAST / Resolution: 1.56→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20112 0 4 1970 22086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00620596
X-RAY DIFFRACTIONf_angle_d0.818228014
X-RAY DIFFRACTIONf_chiral_restr0.05473114
X-RAY DIFFRACTIONf_plane_restr0.00483668
X-RAY DIFFRACTIONf_dihedral_angle_d8.04632754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.55631070.575719193X-RAY DIFFRACTION76.32
1.6-1.640.56111350.531124120X-RAY DIFFRACTION95.93
1.64-1.690.4621420.481724773X-RAY DIFFRACTION98.29
1.69-1.740.43731430.426624816X-RAY DIFFRACTION98.83
1.74-1.810.44151420.383424908X-RAY DIFFRACTION98.99
1.81-1.880.38071480.347524816X-RAY DIFFRACTION98.63
1.88-1.960.31361350.310224532X-RAY DIFFRACTION97.42
1.96-2.070.25851450.241524859X-RAY DIFFRACTION98.81
2.07-2.20.2541450.219924938X-RAY DIFFRACTION98.94
2.2-2.370.23731430.199924947X-RAY DIFFRACTION99.02
2.37-2.60.27921400.200224906X-RAY DIFFRACTION98.86
2.6-2.980.24321410.197124651X-RAY DIFFRACTION97.69
2.98-3.750.23761430.169825093X-RAY DIFFRACTION99.24
3.75-29.020.17081460.151124822X-RAY DIFFRACTION97.54

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