8GCW

Stx2A1(Y77A)-P6 peptide

PDB DOI: https://doi.org/10.2210/pdb8GCW/pdb

Classification: TOXIN
Organism(s): Escherichia coli
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2023-03-03 Released: 2024-03-06
Deposition Author(s): Rudolph, M.J., Li, X.P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.322
R-Value Work: 0.263
R-Value Observed: 0.266

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of the Stx2A1(Y77A) in complex with P6 peptide.

Rudolph, M.J., Li, X.P.

To be published.

Macromolecule Content

Total Structure Weight: 28.52 kDa
Atom Count: 1,927
Modelled Residue Count: 245
Deposited Residue Count: 256
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA N-glycosylase	A	250	Escherichia coli	Mutation(s): 1 Gene Names: stx2A
UniProt
Find proteins for Q8XBV2 (Escherichia coli) Explore Q8XBV2 Go to UniProtKB: Q8XBV2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8XBV2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P stalk protein	B [auth P]	6	Escherichia coli	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.322
R-Value Work: 0.263
R-Value Observed: 0.266
Space Group: P 4₂ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.917	α = 90
b = 117.917	β = 90
c = 117.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI141635-01A1

Revision History (Full details and data files)

Version 1.0: 2024-03-06
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.