8CO2 | pdb_00008co2

YdaS N-terminal domain from prophage CP-933P in E. coli O157:H7

PDB DOI: https://doi.org/10.2210/pdb8CO2/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli O157
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-26 Released: 2023-03-08
Deposition Author(s): Prolic-Kalinsek, M., Loris, R.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

YdaS from the Escherichia coli cryptic prophage CP-933P forms an evolutionary link between Cro repressors and HigA antitoxins

Prolic-Kalinsek, M., Volkov, A.N., Hadzi, S., Bervoets, I., Loris, R.

To be published.

Macromolecule Content

Total Structure Weight: 21.23 kDa
Atom Count: 1,233
Modelled Residue Count: 153
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative antirepressor protein Cro	A, B	94	Escherichia coli O157	Mutation(s): 0 Gene Names: A2F99_004475
UniProt
Find proteins for A0A0D7C0Q9 (Escherichia coli) Explore A0A0D7C0Q9 Go to UniProtKB: A0A0D7C0Q9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0D7C0Q9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.212 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.71	α = 90
b = 42.71	β = 90
c = 65.09	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Prolic-Kalinsek, M.

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G.0033.20N
Research Foundation - Flanders (FWO)	Belgium	G.0226.17N

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

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.