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- PDB-8ewt: Bile salt hydrolase A from Lactobacillus gasseri bound to covalen... -

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Basic information

Entry
Database: PDB / ID: 8ewt
TitleBile salt hydrolase A from Lactobacillus gasseri bound to covalent probe
ComponentsConjugated bile salt hydrolase
KeywordsHYDROLASE / bile salt hydrolase
Function / homology
Function and homology information


chenodeoxycholoyltaurine hydrolase / choloylglycine hydrolase / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / 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
Chem-X3I / Conjugated bile acid hydrolase
Similarity search - Component
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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: To Be Published
Title: Structural diversity of bile salt hydrolases reveals rationale for substrate selectivity
Authors: Walker, M.E. / Redinbo, M.R.
History
DepositionOct 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conjugated bile salt hydrolase
B: Conjugated bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6286
Polymers71,7212
Non-polymers9074
Water3,207178
1
A: Conjugated bile salt hydrolase
B: Conjugated bile salt hydrolase
hetero molecules

A: Conjugated bile salt hydrolase
B: Conjugated bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,25612
Polymers143,4414
Non-polymers1,8158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area16400 Å2
ΔGint-162 kcal/mol
Surface area42250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.440, 108.440, 161.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Conjugated bile salt hydrolase


Mass: 35860.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus gasseri (bacteria) / Gene: LGAS_0054 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A805Z5R7
#2: Chemical ChemComp-X3I / (5R)-5-{(1R,3aS,3bR,5aR,7R,9aS,9bS,11aR)-9a,11a-dimethyl-7-[(prop-2-yn-1-yl)oxy]hexadecahydro-1H-cyclopenta[a]phenanthren-1-yl}-1-fluorohexan-2-one (non-preferred name)


Mass: 430.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H43FO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 4000, 20% (v/v) isopropanol. Protein was incubated with probe and then concentrated to 7.08 mg/mL. Protein crystallized in a 1:2 protein:crystallant ratio.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.03→48.22 Å / Num. obs: 62279 / % possible obs: 96.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.42 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.2126 / Rpim(I) all: 0.0838 / Rrim(I) all: 0.2302 / Net I/σ(I): 6.08
Reflection shellResolution: 2.03→2.103 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.811 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5470 / CC1/2: 0.146 / Rpim(I) all: 0.9079 / Rrim(I) all: 2.044 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SVF

7svf


Resolution: 2.03→48.22 Å / SU ML: 0.2565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 1999 3.27 %
Rwork0.1859 59190 -
obs0.1872 61189 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.43 Å2
Refinement stepCycle: LAST / Resolution: 2.03→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 58 178 5215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695172
X-RAY DIFFRACTIONf_angle_d0.82697057
X-RAY DIFFRACTIONf_chiral_restr0.0533781
X-RAY DIFFRACTIONf_plane_restr0.0055903
X-RAY DIFFRACTIONf_dihedral_angle_d7.4234733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.33291230.31373671X-RAY DIFFRACTION85.39
2.08-2.130.2841360.29513998X-RAY DIFFRACTION92.84
2.13-2.190.33461380.26824084X-RAY DIFFRACTION95.33
2.19-2.270.31651400.25714139X-RAY DIFFRACTION95.98
2.27-2.350.27471410.24144173X-RAY DIFFRACTION96.73
2.35-2.440.29491420.22054203X-RAY DIFFRACTION97.68
2.44-2.550.26791440.21414245X-RAY DIFFRACTION97.95
2.55-2.690.26361430.20174259X-RAY DIFFRACTION98.19
2.69-2.850.23181460.18994305X-RAY DIFFRACTION98.36
2.85-3.070.24241440.18374282X-RAY DIFFRACTION98.64
3.08-3.380.22971480.16514360X-RAY DIFFRACTION99.32
3.38-3.870.18651480.16274396X-RAY DIFFRACTION99.65
3.87-4.880.19261500.16044442X-RAY DIFFRACTION99.61
4.88-48.220.20291560.17314633X-RAY DIFFRACTION98.74

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