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

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Basic information

Entry
Database: PDB / ID: 8etk
TitleBile salt hydrolase A from Lactobacillus gasseri bound to covalent probe
ComponentsConjugated bile salt hydrolase
KeywordsHYDROLASE / bile salt hydrolase
Function / homology: / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / hydrolase activity / Chem-WU9 / Conjugated bile salt hydrolase related amidase
Function and homology information
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWalker, M.E. / Grundy, M.K. / 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. / Grundy, M.K. / Redinbo, M.R.
History
DepositionOct 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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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)72,8508
Polymers71,7212
Non-polymers1,1296
Water3,459192
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)145,70016
Polymers143,4414
Non-polymers2,25912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)108.538, 108.538, 160.341
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
Components on special symmetry positions
IDModelComponents
11A-403-

NA

21B-402-

NA

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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-WU9 / (5R)-5-[(1R,3aS,3bR,5aR,7R,9aS,9bS,11aR)-9a,11a-dimethyl-7-(2-{2-[(prop-2-yn-1-yl)oxy]ethoxy}ethoxy)hexadecahydro-1H-cyclopenta[a]phenanthren-1-yl]-1-fluorohexan-2-one (non-preferred name)


Mass: 518.743 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H51FO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium phosphate dibasic:citric acid, pH 4.2, 40% (v/v) PEG 300. Probe was incubated with protein before tray setup at 6.94 mg/mL protein concentration. Crystals formed in a 1:1 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: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.83→48.54 Å / Num. obs: 84823 / % possible obs: 99.9 % / Redundancy: 14.5 % / Biso Wilson estimate: 34.38 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1765 / Rpim(I) all: 0.04826 / Rrim(I) all: 0.1831 / Net I/σ(I): 12.09
Reflection shellResolution: 1.83→1.895 Å / Redundancy: 14.9 % / Rmerge(I) obs: 4.355 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 8358 / CC1/2: 0.357 / CC star: 0.725 / Rpim(I) all: 1.166 / Rrim(I) all: 4.51 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SVF

7svf


Resolution: 1.83→48.54 Å / SU ML: 0.2611 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 1999 2.36 %
Rwork0.1998 82815 -
obs0.2004 84814 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.55 Å2
Refinement stepCycle: LAST / Resolution: 1.83→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 0 78 192 5181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00755119
X-RAY DIFFRACTIONf_angle_d0.89836988
X-RAY DIFFRACTIONf_chiral_restr0.059777
X-RAY DIFFRACTIONf_plane_restr0.0066893
X-RAY DIFFRACTIONf_dihedral_angle_d13.86571796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.40831400.36235830X-RAY DIFFRACTION99.98
1.88-1.930.34471410.31645830X-RAY DIFFRACTION99.97
1.93-1.980.32011410.27515821X-RAY DIFFRACTION100
1.98-2.050.25061420.24495853X-RAY DIFFRACTION100
2.05-2.120.25051400.23355832X-RAY DIFFRACTION100
2.12-2.210.25291430.22545870X-RAY DIFFRACTION100
2.21-2.310.22911390.20575858X-RAY DIFFRACTION99.97
2.31-2.430.21351420.19715872X-RAY DIFFRACTION100
2.43-2.580.27261430.20075895X-RAY DIFFRACTION100
2.58-2.780.23471430.25918X-RAY DIFFRACTION100
2.78-3.060.22921420.19885914X-RAY DIFFRACTION100
3.06-3.50.20991450.1925990X-RAY DIFFRACTION100
3.5-4.410.19041450.17876029X-RAY DIFFRACTION99.98
4.41-48.540.2061530.18236303X-RAY DIFFRACTION99.95

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