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- PDB-8esl: Bile Salt Hydrolase from a Bacteroidales species with covalent in... -

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Basic information

Entry
Database: PDB / ID: 8esl
TitleBile Salt Hydrolase from a Bacteroidales species with covalent inhibitor bound
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / bile salt hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyChem-WSR
Function and homology information
Biological speciesBacteroidales (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 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 14, 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

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Assembly

Deposited unit
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
C: Choloylglycine hydrolase
D: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,4388
Polymers149,5484
Non-polymers1,8914
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: oligomeric state was observed from the crystal structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-53 kcal/mol
Surface area41060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.142, 66.812, 321.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Choloylglycine hydrolase


Mass: 37386.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroidales (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-WSR / (1R,3aS,3bR,5aR,7R,9aS,9bS,11aR)-1-[(2R)-6-fluoro-5-oxohexan-2-yl]-9a,11a-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-7-yl hydrogen sulfate (non-preferred name)


Mass: 472.653 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H41FO5S / Feature type: SUBJECT OF INVESTIGATION
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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES: NaOH, pH 7.5, 25% (w/v) PEG 1000. 50 mL protein at 2.5 uM was incubated with 50 uM inhibitor for 1h at 37oC. Mixture was washed 3x with buffer in a spin concentrator and then ...Details: 0.1 M HEPES: NaOH, pH 7.5, 25% (w/v) PEG 1000. 50 mL protein at 2.5 uM was incubated with 50 uM inhibitor for 1h at 37oC. Mixture was washed 3x with buffer in a spin concentrator and then concentrated to 6.77 mg/mL final concentration. Crystals formed in conditions with 1:2 ratio of protein:mother liquor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→45.07 Å / Num. obs: 24835 / % possible obs: 94.77 % / Redundancy: 3.4 % / Biso Wilson estimate: 92.36 Å2 / CC1/2: 0.978 / CC star: 0.994 / Rmerge(I) obs: 0.2399 / Rpim(I) all: 0.1551 / Rrim(I) all: 0.2875 / Net I/σ(I): 3.81
Reflection shellResolution: 3.11→3.221 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.71 / Mean I/σ(I) obs: 0.74 / Num. unique obs: 2378 / CC1/2: 0.121 / CC star: 0.464 / Rpim(I) all: 1.115 / Rrim(I) all: 2.057 / % possible all: 80.39

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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: AlphaFold2 model of the protein

Resolution: 3.11→45.07 Å / SU ML: 0.5378 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.9647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3051 2001 8.28 %
Rwork0.2769 22153 -
obs0.2769 24154 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.79 Å2
Refinement stepCycle: LAST / Resolution: 3.11→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8852 0 124 0 8976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00189225
X-RAY DIFFRACTIONf_angle_d0.409912691
X-RAY DIFFRACTIONf_chiral_restr0.04031469
X-RAY DIFFRACTIONf_plane_restr0.00431596
X-RAY DIFFRACTIONf_dihedral_angle_d5.7151404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.190.41831200.38251314X-RAY DIFFRACTION78.66
3.19-3.270.40731340.33811373X-RAY DIFFRACTION86.16
3.27-3.370.35131170.3371494X-RAY DIFFRACTION90.71
3.37-3.480.36611340.35631557X-RAY DIFFRACTION94.36
3.48-3.60.37211560.33861552X-RAY DIFFRACTION96.28
3.6-3.750.33361320.31861654X-RAY DIFFRACTION98.46
3.75-3.920.37941610.30261613X-RAY DIFFRACTION98.83
3.92-4.120.33531340.30231611X-RAY DIFFRACTION98.09
4.12-4.380.29191470.27821601X-RAY DIFFRACTION96.36
4.38-4.720.30431460.23821624X-RAY DIFFRACTION97.63
4.72-5.20.30231530.25941663X-RAY DIFFRACTION98.75
5.2-5.940.31711570.2811652X-RAY DIFFRACTION98.69
5.95-7.480.27791470.28611703X-RAY DIFFRACTION98.2
7.49-45.070.23131630.21981742X-RAY DIFFRACTION95.92

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