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

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Basic information

Entry
Database: PDB / ID: 8etf
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
NICKEL (II) ION / Chem-WU5 / choloylglycine hydrolase
Similarity search - Component
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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
H: Choloylglycine hydrolase
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
C: Choloylglycine hydrolase
D: Choloylglycine hydrolase
E: Choloylglycine hydrolase
F: Choloylglycine hydrolase
G: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,31918
Polymers297,0618
Non-polymers3,25810
Water24,7171372
1
H: Choloylglycine hydrolase
B: Choloylglycine hydrolase
hetero molecules

D: Choloylglycine hydrolase
E: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1609
Polymers148,5314
Non-polymers1,6295
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
2
A: Choloylglycine hydrolase
C: Choloylglycine hydrolase
F: Choloylglycine hydrolase
G: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1609
Polymers148,5314
Non-polymers1,6295
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.523, 147.994, 104.563
Angle α, β, γ (deg.)90.000, 94.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Choloylglycine hydrolase


Mass: 37132.645 Da / Num. of mol.: 8
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-WU5 / (5R)-1-fluoro-5-[(1R,3aS,3bR,5aR,7R,9aS,9bS,11aR)-7-hydroxy-9a,11a-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-1-yl]hexan-2-one (non-preferred name)


Mass: 392.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C25H41FO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1372 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M proline, 0.1M HEPES:NaOH, pH 7.5, 10% (w/v) PEG 3350. Crystals grew in a 2:1 protein:crystallant ratio at a 11.4 mg/mL final protein concentration. Inhibitor was incubated with protein prior to tray setup.

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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: 1.79→45.86 Å / Num. obs: 296253 / % possible obs: 99.51 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.47 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1344 / Rpim(I) all: 0.06826 / Rrim(I) all: 0.1344 / Net I/σ(I): 6.43
Reflection shellResolution: 1.79→1.854 Å / Redundancy: 3.8 % / Rmerge(I) obs: 2.275 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 29558 / CC1/2: 0.195 / CC star: 0.572 / Rpim(I) all: 1.331 / Rrim(I) all: 2.645 / % possible all: 97.73

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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: 1.79→45.86 Å / SU ML: 0.2688 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2218 2004 0.68 %
Rwork0.1865 293476 -
obs0.1868 295480 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.66 Å2
Refinement stepCycle: LAST / Resolution: 1.79→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20090 0 218 1372 21680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007320835
X-RAY DIFFRACTIONf_angle_d0.904628437
X-RAY DIFFRACTIONf_chiral_restr0.05963207
X-RAY DIFFRACTIONf_plane_restr0.00663687
X-RAY DIFFRACTIONf_dihedral_angle_d14.13137393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.3581470.356220500X-RAY DIFFRACTION97.42
1.83-1.880.3551210.329220734X-RAY DIFFRACTION98.99
1.88-1.940.32791510.30121023X-RAY DIFFRACTION99.89
1.94-20.30961520.285820942X-RAY DIFFRACTION99.93
2-2.070.26741450.25120942X-RAY DIFFRACTION99.8
2.07-2.160.28881500.241221049X-RAY DIFFRACTION99.85
2.16-2.260.26711350.226820961X-RAY DIFFRACTION99.84
2.26-2.370.26461430.217121064X-RAY DIFFRACTION99.82
2.37-2.520.27251470.211920938X-RAY DIFFRACTION99.77
2.52-2.720.25961400.199721034X-RAY DIFFRACTION99.73
2.72-2.990.21731380.192821029X-RAY DIFFRACTION99.69
2.99-3.420.23691490.178920996X-RAY DIFFRACTION99.62
3.42-4.310.17741380.150421013X-RAY DIFFRACTION99.3
4.31-45.860.15831480.136921251X-RAY DIFFRACTION99.6

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