2RLC | pdb_00002rlc

Crystal Structure of the Conjugated Bile Acid Hydrolase from Clostridium perfringens in Complex with Reaction Products Glycine and Cholate

• PDB DOI: https://doi.org/10.2210/pdb2RLC/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-18 Released: 2009-02-17 
• Deposition Author(s): Rossmann, M., Saenger, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structures of choloyl glycine hydrolase from Clostridium perfringens

Rossmann, M., Saenger, W.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.19 kDa 
• Atom Count: 3,050 
• Modeled Residue Count: 328 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choloylglycine hydrolase	A	328	Clostridium perfringens	Mutation(s): 0  Gene Names: cbh EC: 3.5.1.24 (PDB Primary Data), 3.5.1 (UniProt), 2.3.1 (UniProt)
UniProt
Find proteins for P54965 (Clostridium perfringens (strain 13 / Type A)) Explore P54965  Go to UniProtKB:  P54965

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CHD	D [auth A]	CHOLIC ACID C24 H40 O5 BHQCQFFYRZLCQQ-OELDTZBJSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GLY	E [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.24	α = 90
b = 64.24	β = 90
c = 169.9	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Rossmann, M., Saenger, W.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary