2RF8 | pdb_00002rf8

Crystal Structure of the mutant C2A conjugated bile acid hydrolase from Clostridium perfringens

PDB DOI: https://doi.org/10.2210/pdb2RF8/pdb

Classification: HYDROLASE
Organism(s): Clostridium perfringens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-09-28 Released: 2008-10-07
Deposition Author(s): Rossmann, M., Saenger, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.275 (Depositor), 0.264 (DCC)
R-Value Work:
0.206 (Depositor), 0.198 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Structural basis for the catalytic activity and processing of the conjugated bile salt hydrolase from Clostridium perfringens

Rossmann, M., Saenger, W.

To be published.

Macromolecule Content

Total Structure Weight: 74.65 kDa
Atom Count: 5,454
Modeled Residue Count: 657
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choloylglycine hydrolase	A, B	329	Clostridium perfringens	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54965
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.275 (Depositor), 0.264 (DCC)
R-Value Work: 0.206 (Depositor), 0.198 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.64	α = 90
b = 64.64	β = 90
c = 338.833	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, 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.