8ESL | pdb_00008esl

Bile Salt Hydrolase from a Bacteroidales species with covalent inhibitor bound

PDB DOI: https://doi.org/10.2210/pdb8ESL/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Bacteroidales
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-14 Released: 2023-11-01
Deposition Author(s): Walker, M.E., Redinbo, M.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.305 (Depositor), 0.305 (DCC)
R-Value Work:
0.277 (Depositor), 0.277 (DCC)
R-Value Observed:
0.277 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural diversity of bile salt hydrolases reveals rationale for substrate selectivity

Walker, M.E., Redinbo, M.R.

To be published.

Macromolecule Content

Total Structure Weight: 151.44 kDa
Atom Count: 8,976
Modeled Residue Count: 1,204
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choloylglycine hydrolase	A, B, C, D	338	Bacteroidales	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WSR (Subject of Investigation/LOI) Query on WSR Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	(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) C₂₅ H₄₁ F O₅ S MVPISWRWXKQVBV-CIQXVCGBSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.305 (Depositor), 0.305 (DCC)
R-Value Work: 0.277 (Depositor), 0.277 (DCC)
R-Value Observed: 0.277 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.142	α = 90
b = 66.812	β = 90
c = 321.831	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM135218

Revision History (Full details and data files)

Version 1.0: 2023-11-01
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.