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- PDB-7svk: Bile Salt Hydrolase from Lactobacillus reuteri -

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Basic information

Entry
Database: PDB / ID: 7svk
TitleBile Salt Hydrolase from Lactobacillus reuteri
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 reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsWalker, M.E. / Beaty, V.V. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3505
Polymers36,9651
Non-polymers3844
Water3,873215
1
A: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,39820
Polymers147,8614
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area22180 Å2
ΔGint-293 kcal/mol
Surface area41310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.260, 176.682, 42.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

#1: Protein Choloylglycine hydrolase


Mass: 36965.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Gene: LRLP16767_LR202_00948 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U5F994, choloylglycine hydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris Propane:HCl, pH 7.0, 1.5 M Ammonium Sulfate. Crystals formed in 2:1 ratio protein (13.3 mg/mL) to mother liquor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→45.2 Å / Num. obs: 62633 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 25.84 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.0372 / Rrim(I) all: 0.053 / Net I/σ(I): 10.7
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 2 % / Rmerge(I) obs: 1.282 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6177 / CC1/2: 0.414 / CC star: 0.765 / Rpim(I) all: 1.282 / Rrim(I) all: 1.813 / % possible all: 99

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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: 1.66→45.2 Å / SU ML: 0.2635 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2255 1998 3.2 %
Rwork0.2012 60490 -
obs0.202 62488 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.75 Å2
Refinement stepCycle: LAST / Resolution: 1.66→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 20 215 2752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652616
X-RAY DIFFRACTIONf_angle_d0.84983575
X-RAY DIFFRACTIONf_chiral_restr0.0587394
X-RAY DIFFRACTIONf_plane_restr0.006473
X-RAY DIFFRACTIONf_dihedral_angle_d11.3385356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.44951400.43494231X-RAY DIFFRACTION98.87
1.7-1.750.41411410.40584260X-RAY DIFFRACTION99.55
1.75-1.80.40141400.38074261X-RAY DIFFRACTION99.73
1.8-1.860.33131410.34174260X-RAY DIFFRACTION99.84
1.86-1.920.34561410.28984277X-RAY DIFFRACTION99.73
1.92-20.27211420.24714276X-RAY DIFFRACTION99.64
2-2.090.25641420.21564285X-RAY DIFFRACTION99.71
2.09-2.20.26421420.2034308X-RAY DIFFRACTION99.87
2.2-2.340.231420.19284308X-RAY DIFFRACTION99.89
2.34-2.520.23631430.1884325X-RAY DIFFRACTION99.91
2.52-2.770.26151430.18894322X-RAY DIFFRACTION99.89
2.77-3.180.2171430.18974368X-RAY DIFFRACTION100
3.18-40.16411460.16574409X-RAY DIFFRACTION99.96
4-45.20.17591520.16554600X-RAY DIFFRACTION99.77

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