6M8O | pdb_00006m8o

Crystal structure of the receiver domain of LytR from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb6M8O/pdb

Classification: SIGNALING PROTEIN
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-08-22 Released: 2018-09-19
Deposition Author(s): Shala-Lawrence, A., Audette, G.F.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.237 (Depositor), 0.247 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6M8O

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the receiver domain of LytR from Staphylococcus aureus

Shala-Lawrence, A., Audette, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 15.14 kDa
Atom Count: 948
Modeled Residue Count: 118
Deposited Residue Count: 134
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator	A	134	Staphylococcus aureus	Mutation(s): 0 Gene Names: C3B39_09020, EP54_06415, EQ90_12235, HMPREF3211_02791
UniProt
Find proteins for P60611 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P60611 Go to UniProtKB: P60611
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60611
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.237 (Depositor), 0.247 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.201 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.747	α = 90
b = 84.747	β = 90
c = 157.304	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASES	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-09-19

Deposition Author(s):

Shala-Lawrence, A.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-06218-2014

Revision History (Full details and data files)

Version 1.0: 2018-09-19
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.