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- PDB-7svg: Bile Salt Hydrolase A from Lactobacillus gasseri with chenodeoxyc... -

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Basic information

Entry
Database: PDB / ID: 7svg
TitleBile Salt Hydrolase A from Lactobacillus gasseri with chenodeoxycholate and taurine bound
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / bile salt hydrolase
Function / homologyCHENODEOXYCHOLIC ACID / 2-AMINOETHANESULFONIC ACID / :
Function and homology information
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,31111
Polymers143,6334
Non-polymers1,6787
Water24,9691386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18810 Å2
ΔGint-106 kcal/mol
Surface area42290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.147, 153.115, 94.979
Angle α, β, γ (deg.)90.000, 105.795, 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: 35908.262 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-JN3 / CHENODEOXYCHOLIC ACID / (3ALPHA,5ALPHA,7BETA,8ALPHA,17ALPHA)-3,7-DIHYDROXYCHOLAN-24-OIC ACID


Mass: 392.572 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1386 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3 streak seeded with crystals grown in 20% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3. Crystals were grown in a protein (9.55 mg/mL):mother ...Details: 18% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3 streak seeded with crystals grown in 20% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3. Crystals were grown in a protein (9.55 mg/mL):mother liquor ratio of 1:2. Crystal seeds were streaked into this condition from a broad screen hit and then the resultant crystals were soaked in 1:1 ratio of mother liquor:100 mM TCDCA for 24h before looping.

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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: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→29.34 Å / Num. obs: 332715 / % possible obs: 92.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.08 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.09959 / Rpim(I) all: 0.05829 / Rrim(I) all: 0.1158 / Net I/σ(I): 6.16
Reflection shellResolution: 1.352→1.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.518 / Mean I/σ(I) obs: 0.44 / Num. unique obs: 29313 / CC1/2: 0.317 / CC star: 0.694 / Rpim(I) all: 0.9715 / Rrim(I) all: 1.814 / % possible all: 72.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HEZ

2hez


Resolution: 1.35→29.34 Å / SU ML: 0.2517 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2 1965 0.6 %
Rwork0.1777 325823 -
obs0.1778 327788 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.19 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9783 0 112 1386 11281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006210145
X-RAY DIFFRACTIONf_angle_d0.857813851
X-RAY DIFFRACTIONf_chiral_restr0.0831535
X-RAY DIFFRACTIONf_plane_restr0.00561773
X-RAY DIFFRACTIONf_dihedral_angle_d8.38021376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.390.4329920.431916582X-RAY DIFFRACTION66.32
1.39-1.420.39161380.41922255X-RAY DIFFRACTION89.09
1.42-1.470.40041440.391623033X-RAY DIFFRACTION92.08
1.47-1.510.41081420.384723354X-RAY DIFFRACTION93.27
1.51-1.570.34991460.317623491X-RAY DIFFRACTION94.06
1.57-1.630.30741420.25623604X-RAY DIFFRACTION94.43
1.63-1.70.25611470.228823740X-RAY DIFFRACTION94.82
1.7-1.790.24321370.215223847X-RAY DIFFRACTION95.11
1.79-1.910.20461500.181823956X-RAY DIFFRACTION95.63
1.91-2.050.18811380.163924058X-RAY DIFFRACTION96.24
2.05-2.260.18331470.157824207X-RAY DIFFRACTION96.5
2.26-2.590.18011500.158624328X-RAY DIFFRACTION97.16
2.59-3.260.15761460.15324556X-RAY DIFFRACTION97.6
3.26-29.340.16571460.136324812X-RAY DIFFRACTION98.15

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