8S0U

Structure of the LytM domain of PrgK from E. faecalis

PDB DOI: https://doi.org/10.2210/pdb8S0U/pdb

Classification: HYDROLASE
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-02-14 Released: 2024-02-28
Deposition Author(s): Sun, W.-S., Berntsson, R.P.-A.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.208
R-Value Work: 0.177
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

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

Literature

Breaking Barriers: pCF10 Type 4 Secretion System relies on a self-regulating muramidase to modulate the cell wall

Sun, W.-S., Torrens, G., ter Beek, J., Cava, F., Berntsson, R.P.-A.

To be published.

Macromolecule Content

Total Structure Weight: 60.7 kDa
Atom Count: 4,961
Modelled Residue Count: 514
Deposited Residue Count: 522
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PrgK	A, B	261	Enterococcus faecalis	Mutation(s): 0 Gene Names: prgK
UniProt
Find proteins for Q5G3P4 (Enterococcus faecalis) Explore Q5G3P4 Go to UniProtKB: Q5G3P4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5G3P4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.208
R-Value Work: 0.177
R-Value Observed: 0.177
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.32	α = 63.3
b = 53.69	β = 70.37
c = 56.35	γ = 70.16

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-28

Deposition Author(s):

Berntsson, R.P.-A.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-03599
Swedish Research Council	Sweden	2023-02423

Revision History (Full details and data files)

Version 1.0: 2024-02-28
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.