8CB4

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with tripeptide Leu-Leu-Leu

PDB DOI: https://doi.org/10.2210/pdb8CB4/pdb

Classification: TRANSCRIPTION
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-01-25 Released: 2024-08-07
Deposition Author(s): Oelker, M., Sauer-Eriksson, A.E.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.277
R-Value Work: 0.208
R-Value Observed: 0.211

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of promiscuous inhibition of virulence activator PrfA by nutritional peptides

Oelker, M., Lindgren, C., Grundstrom, C., Krypotou, E., Scortti, M., Hainzl, T., Vazquez-Boland, J., Sauer-Eriksson, A.E.

To be published.

Macromolecule Content

Total Structure Weight: 55.68 kDa
Atom Count: 3,858
Modelled Residue Count: 463
Deposited Residue Count: 484
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Listeriolysin regulatory protein	A, B	239	Listeria monocytogenes	Mutation(s): 0 Gene Names: prfA, lmo0200
UniProt
Find proteins for P22262 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P22262 Go to UniProtKB: P22262
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22262
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tripeptide LEU-LEU-LEU	C, D	3	Listeria monocytogenes	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.277
R-Value Work: 0.208
R-Value Observed: 0.211
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.099	α = 90
b = 86.785	β = 90
c = 115.864	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Sauer-Eriksson, A.E.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2015-03607
Swedish Research Council	Sweden	2019-03771

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release

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 R01GM133198.