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), 0.217 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 153
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.217 (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

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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

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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.