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- PDB-8esg: Bile Salt Hydrolase B from Lactobacillus gasseri with covalent in... -

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Basic information

Entry
Database: PDB / ID: 8esg
TitleBile Salt Hydrolase B from Lactobacillus gasseri with covalent inhibitor bound
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / bile salt hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


choloylglycine hydrolase / lipid metabolic process / hydrolase activity / metal ion binding
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-WSR / choloylglycine hydrolase
Similarity search - Component
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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
Revision 1.1Nov 13, 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: Choloylglycine hydrolase
H: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2114
Polymers74,2652
Non-polymers9452
Water00
1
A: Choloylglycine hydrolase
H: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
H: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,4218
Polymers148,5314
Non-polymers1,8914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area17630 Å2
ΔGint-91 kcal/mol
Surface area42030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.362, 157.362, 140.718
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Choloylglycine hydrolase


Mass: 37132.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus gasseri (bacteria) / Gene: F8244_03005 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A833FHE1
#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.: 2 / Source method: obtained synthetically / Formula: C25H41FO5S / Feature type: SUBJECT OF INVESTIGATION
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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH, pH 10.5, 2M Ammonium Sulfate. Crystals formed in a 2:1 ratio of protein:mother liquor. 2.5 uM protein was incubated with 50 uM inhibitor for 1h at ...Details: 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH, pH 10.5, 2M Ammonium Sulfate. Crystals formed in a 2:1 ratio of protein:mother liquor. 2.5 uM protein was incubated with 50 uM inhibitor for 1h at 37oC. Mixture was washed 3x with buffer in a spin concentrator and then concentrated to 8 mg/mL final concentration.

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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: Aug 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.18→48.95 Å / Num. obs: 100941 / % possible obs: 99.8 % / Redundancy: 20.8 % / Biso Wilson estimate: 63.96 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.028 / Rrim(I) all: 0.128 / Net I/σ(I): 16.7
Reflection shellResolution: 2.18→2.258 Å / Redundancy: 21.7 % / Rmerge(I) obs: 6.367 / Mean I/σ(I) obs: 0.57 / Num. unique obs: 5296 / CC1/2: 0.209 / CC star: 0.588 / Rpim(I) all: 1.38 / Rrim(I) all: 6.518 / % possible all: 98.6

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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: 7SVH

7svh


Resolution: 2.18→48.95 Å / SU ML: 0.4593 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.6343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2551 3753 3.72 %
Rwork0.2359 97188 -
obs0.2366 100941 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.93 Å2
Refinement stepCycle: LAST / Resolution: 2.18→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 62 0 4978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00175101
X-RAY DIFFRACTIONf_angle_d0.46646972
X-RAY DIFFRACTIONf_chiral_restr0.0426791
X-RAY DIFFRACTIONf_plane_restr0.0029907
X-RAY DIFFRACTIONf_dihedral_angle_d6.4014736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.40491310.42173228X-RAY DIFFRACTION88.35
2.21-2.240.42261380.40923403X-RAY DIFFRACTION94.6
2.24-2.270.42611300.40263589X-RAY DIFFRACTION98.49
2.27-2.30.4431380.39313584X-RAY DIFFRACTION99.17
2.3-2.330.39331420.39173631X-RAY DIFFRACTION99.6
2.33-2.370.42141460.37943608X-RAY DIFFRACTION99.6
2.37-2.410.34811340.37523593X-RAY DIFFRACTION99.79
2.41-2.450.36561380.3493640X-RAY DIFFRACTION100
2.45-2.50.41971450.34883621X-RAY DIFFRACTION99.84
2.5-2.540.39811400.33983646X-RAY DIFFRACTION100
2.54-2.60.34381360.33323607X-RAY DIFFRACTION99.92
2.6-2.650.38091390.32523606X-RAY DIFFRACTION100
2.65-2.710.32211390.31543665X-RAY DIFFRACTION100
2.71-2.780.32181370.31253630X-RAY DIFFRACTION100
2.78-2.860.37841400.31543605X-RAY DIFFRACTION99.95
2.86-2.940.36351350.30943605X-RAY DIFFRACTION100
2.94-3.040.28451410.2893633X-RAY DIFFRACTION99.95
3.04-3.140.31481430.30213646X-RAY DIFFRACTION100
3.14-3.270.29911390.27783608X-RAY DIFFRACTION100
3.27-3.420.27181430.25963645X-RAY DIFFRACTION100
3.42-3.60.2931420.23893601X-RAY DIFFRACTION100
3.6-3.820.2161410.22913640X-RAY DIFFRACTION100
3.82-4.120.24911360.21343630X-RAY DIFFRACTION100
4.12-4.530.18991420.18063639X-RAY DIFFRACTION100
4.53-5.190.17621400.17123616X-RAY DIFFRACTION100
5.19-6.530.21961400.20273635X-RAY DIFFRACTION100
6.54-48.950.20151380.17853634X-RAY DIFFRACTION99.95

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