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- PDB-8blt: Structure of Lactobacillus salivarius (Ls) bile salt hydrolase(BS... -

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Basic information

Entry
Database: PDB / ID: 8blt
TitleStructure of Lactobacillus salivarius (Ls) bile salt hydrolase(BSH) in complex with taurocholate (TCA)
ComponentsBile salt hydrolase
KeywordsHYDROLASE / Bile salt hydrolase / taurocholate / TCA
Function / homology
Function and homology information


choloylglycine hydrolase activity / choloylglycine hydrolase / lipid metabolic process
Similarity search - Function
: / : / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
TAUROCHOLIC ACID / choloylglycine hydrolase
Similarity search - Component
Biological speciesLigilactobacillus salivarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKarlov, D.S. / Long, S.L. / Zeng, X. / Xu, F. / Lal, K. / Cao, L. / Hayoun, K. / Lin, J. / Joyce, S.A. / Tikhonova, I.G.
Funding support United States, United Kingdom, 5items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)2018-67015-27475 United States
Other government05935-NAGpro
Other governmentDAFM 17-RD-US-ROI
Other governmentKJCX20220422
Engineering and Physical Sciences Research CouncilEP/R029407/1 and EP/W03204X/1 United Kingdom
CitationJournal: Structure / Year: 2023
Title: Characterization of the mechanism of bile salt hydrolase substrate specificity by experimental and computational analyses.
Authors: Karlov, D.S. / Long, S.L. / Zeng, X. / Xu, F. / Lal, K. / Cao, L. / Hayoun, K. / Lin, J. / Joyce, S.A. / Tikhonova, I.G.
History
DepositionNov 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 17, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Feb 7, 2024Group: 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: Bile salt hydrolase
B: Bile salt hydrolase
C: Bile salt hydrolase
D: Bile salt hydrolase
E: Bile salt hydrolase
F: Bile salt hydrolase
G: Bile salt hydrolase
H: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,60616
Polymers294,4808
Non-polymers4,1268
Water18,4471024
1
A: Bile salt hydrolase
B: Bile salt hydrolase
hetero molecules

G: Bile salt hydrolase
H: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3038
Polymers147,2404
Non-polymers2,0634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area22020 Å2
ΔGint-59 kcal/mol
Surface area44290 Å2
MethodPISA
2
C: Bile salt hydrolase
D: Bile salt hydrolase
E: Bile salt hydrolase
F: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3038
Polymers147,2404
Non-polymers2,0634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22070 Å2
ΔGint-54 kcal/mol
Surface area43710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.759, 94.605, 168.215
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bile salt hydrolase


Mass: 36810.023 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ligilactobacillus salivarius (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J7H3P9
#2: Chemical
ChemComp-TCH / TAUROCHOLIC ACID


Mass: 515.703 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C26H45NO7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1024 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 20% Polyethylene glycol 3350, 0.2M potassium dihydrogen phosphate pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 150183 / % possible obs: 96.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.2 Å2 / Rrim(I) all: 0.105 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 150183 / Rrim(I) all: 0.34

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
PDB_EXTRACTV4.0data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HKE

5hke


Resolution: 2.1→25.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.433 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21264 7772 5.2 %RANDOM
Rwork0.17986 ---
obs0.18158 142049 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.01 Å2
2--0.03 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→25.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20181 0 280 1024 21485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01320917
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719357
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.64428480
X-RAY DIFFRACTIONr_angle_other_deg1.331.57944570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49652541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24824.1091105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.933153377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9351577
X-RAY DIFFRACTIONr_chiral_restr0.0740.22812
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024854
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5742.95810209
X-RAY DIFFRACTIONr_mcbond_other2.5742.95710208
X-RAY DIFFRACTIONr_mcangle_it3.5674.42112735
X-RAY DIFFRACTIONr_mcangle_other3.5674.42212736
X-RAY DIFFRACTIONr_scbond_it3.0393.25510708
X-RAY DIFFRACTIONr_scbond_other3.0393.25410707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4944.7815746
X-RAY DIFFRACTIONr_long_range_B_refined5.94634.29822644
X-RAY DIFFRACTIONr_long_range_B_other5.94134.24122519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 554 -
Rwork0.184 10021 -
obs--92.26 %

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