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- PDB-8vrx: Bile salt hydrolase from Arthrobacter citreus -

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Basic information

Entry
Database: PDB / ID: 8vrx
TitleBile salt hydrolase from Arthrobacter citreus
ComponentsBile Salt Hydrolase
KeywordsHYDROLASE / Bile salt hydrolase
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesArthrobacter citreus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsRuzzini, A. / Dhindwal, P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and functional analysis of a bile salt hydrolase from the bison microbiome.
Authors: Asar, R. / Dhindwal, P. / Ruzzini, A.
History
DepositionJan 22, 2024Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 7, 2024ID: 8U7N
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,25924
Polymers70,6442
Non-polymers1,61522
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-23 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.787, 44.071, 86.592
Angle α, β, γ (deg.)90.00, 111.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-732-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bile Salt Hydrolase


Mass: 35322.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter citreus (bacteria) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 6 types, 643 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 20% PEG 3350, 0.2 M MgCl2, 1 X PBS, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18053 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18053 Å / Relative weight: 1
ReflectionResolution: 2.04→42.42 Å / Num. obs: 37834 / % possible obs: 99.69 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.03277 / Net I/σ(I): 43.41
Reflection shellResolution: 2.044→2.117 Å / Rmerge(I) obs: 0.0837 / Num. unique obs: 3714 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→40.4 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1719 1999 5.28 %
Rwork0.1332 --
obs0.1353 37829 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 103 621 5580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.606
X-RAY DIFFRACTIONf_dihedral_angle_d7.966767
X-RAY DIFFRACTIONf_chiral_restr0.047772
X-RAY DIFFRACTIONf_plane_restr0.004947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.10.19321410.13892529X-RAY DIFFRACTION98
2.1-2.150.17541400.13172511X-RAY DIFFRACTION100
2.15-2.220.17081430.12832559X-RAY DIFFRACTION100
2.22-2.290.21011420.13542534X-RAY DIFFRACTION100
2.29-2.370.20481400.13572524X-RAY DIFFRACTION100
2.37-2.460.19441430.14282554X-RAY DIFFRACTION100
2.46-2.580.21861410.13832534X-RAY DIFFRACTION100
2.58-2.710.19391440.14152564X-RAY DIFFRACTION100
2.71-2.880.17351420.13632552X-RAY DIFFRACTION100
2.88-3.10.16051420.13652559X-RAY DIFFRACTION100
3.1-3.420.14831430.12342550X-RAY DIFFRACTION100
3.42-3.910.14841440.11682583X-RAY DIFFRACTION100
3.91-4.920.14931450.11522605X-RAY DIFFRACTION100
4.92-40.40.1641490.16412672X-RAY DIFFRACTION99

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