5DIM | pdb_00005dim

Mutant toxin in 'native' space group

PDB DOI: https://doi.org/10.2210/pdb5DIM/pdb

Classification: TOXIN
Organism(s): Clostridium perfringens str. 13
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2015-09-01 Released: 2016-11-09
Deposition Author(s): Parker, M.W., Gorman, M.A., Lawrence, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.32 Å
R-Value Free:
0.297 (Depositor), 0.312 (DCC)
R-Value Work:
0.236 (Depositor), 0.252 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of mutant toxin at 3.32 Angstrom resolution

Parker, M.W., Gorman, M.A., Lawrence, S.L., Morton, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 53.01 kDa
Atom Count: 3,692
Modeled Residue Count: 465
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Perfringolysin O	A	472	Clostridium perfringens str. 13	Mutation(s): 1 Gene Names: pfo, pfoA, pfoR, CPE0163 Membrane Entity: Yes
UniProt
Find proteins for P0C2E9 (Clostridium perfringens (strain 13 / Type A)) Explore P0C2E9 Go to UniProtKB: P0C2E9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C2E9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.32 Å
R-Value Free: 0.297 (Depositor), 0.312 (DCC)
R-Value Work: 0.236 (Depositor), 0.252 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.951	α = 90
b = 207.332	β = 90
c = 212.442	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, 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.