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

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Basic information

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


choloylglycine hydrolase / lipid metabolic process / hydrolase activity
Similarity search - Function
: / : / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
GLYCOCHOLIC 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 / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Feb 14, 2024Group: Refinement description / Category: 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)298,67117
Polymers294,4808
Non-polymers4,1919
Water28,3201572
1
A: Bile salt hydrolase
B: Bile salt hydrolase
E: Bile salt hydrolase
F: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1038
Polymers147,2404
Non-polymers1,8624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21430 Å2
ΔGint-57 kcal/mol
Surface area44740 Å2
MethodPISA
2
G: Bile salt hydrolase
H: Bile salt hydrolase
hetero molecules

C: Bile salt hydrolase
D: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5689
Polymers147,2404
Non-polymers2,3285
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area21990 Å2
ΔGint-65 kcal/mol
Surface area44340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.010, 94.090, 166.974
Angle α, β, γ (deg.)90.00, 90.64, 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-GCH / GLYCOCHOLIC ACID / N-CHOLYLGLYCINE


Mass: 465.623 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C26H43NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1572 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
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: 143414 / % possible obs: 94.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.066 / Χ2: 1.096 / Net I/σ(I): 12.5 / Num. measured all: 755182
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.142.60.232128350.995186.7
2.14-2.182.70.211138021.05193.3
2.18-2.222.70.181138051.08193.3
2.22-2.262.70.164140151.081193.8
2.26-2.312.70.155138981.095194.4
2.31-2.372.70.146140631.095194.6
2.37-2.422.70.137140551.082194.6
2.42-2.492.70.121140311.106194.8
2.49-2.562.70.108141561.106195.2
2.56-2.652.70.1141141.106195.4
2.65-2.742.70.089142741.115195.8
2.74-2.852.70.083142231.083196
2.85-2.982.70.074142901.097196.1
2.98-3.142.70.069143431.109196.7
3.14-3.332.70.059143361.107196.8
3.33-3.592.60.054143331.143196.4
3.59-3.952.70.049143381.095196.5
3.95-4.522.70.044140351.132194.9
4.52-5.72.80.044143461.126196.6
5.7-502.90.042143751.099196.8

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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→28.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.769 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19924 7902 5.52 %RANDOM
Rwork0.14668 ---
obs0.14952 135309 94.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.367 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.02 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20210 0 297 1572 22079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01320984
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719441
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.64328565
X-RAY DIFFRACTIONr_angle_other_deg1.341.57944779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.32352545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73324.0681116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.344153401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8291579
X-RAY DIFFRACTIONr_chiral_restr0.0750.22823
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024877
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_it2.1112.6110228
X-RAY DIFFRACTIONr_mcbond_other2.1052.60610209
X-RAY DIFFRACTIONr_mcangle_it2.9383.89612739
X-RAY DIFFRACTIONr_mcangle_other2.9373.89612740
X-RAY DIFFRACTIONr_scbond_it2.9112.91510756
X-RAY DIFFRACTIONr_scbond_other2.912.91510755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3554.26215825
X-RAY DIFFRACTIONr_long_range_B_refined5.67730.74823024
X-RAY DIFFRACTIONr_long_range_B_other5.6230.5422741
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 609 -
Rwork0.15 8890 -
obs--85.65 %

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