Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.36 kDa 
• Atom Count: 1829 
• Modelled Residue Count: 221 
• Deposited Residue Count: 232 
• Unique protein chains: 1

6ITW

Crystal structure of Atu4351 from Agrobacterium tumefaciens

• PDB DOI: 10.2210/pdb6ITW/pdb

• Classification: ANTITOXIN
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-26 Released: 2019-03-20 
• Deposition Author(s): Shi, L., Gao, Z., Zhang, H., Dong, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.250 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 

Literature

Crystal structure of the type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens.

Shi, L., Gao, Z., Zhang, T., Zhang, H., Dong, Y.

(2019) Acta Crystallogr F Struct Biol Commun 75: 153-158

• PubMed: 30839288 
• DOI: 10.1107/S2053230X19000815
• Primary Citation of Related Structures:  
  6ITW


• PubMed Abstract: 
  

The type VI secretion system (T6SS) is a novel multiprotein needle-like apparatus that is distributed widely in Gram-negative bacteria. Bacteria harboring T6SSs inject various effectors into both eukaryotic and prokaryotic cells for interspecies competition or virulence-related processes. The toxicities of the effectors can be neutralized by their cognate immunity proteins. Tde1 (Atu4350)-Tdi1 (Atu4351) has recently been characterized as a T6SS effector-immunity pair in the soil bacterium Agrobacterium tumefaciens and the neutralization mechanism remains unknown. Here, the crystal structure of the immunity protein Tdi1 was determined at 2.40 Å resolution by the single-wavelength anomalous dispersion method. Structural analysis suggested that it is composed of a GAD-like domain and an inserted DUF1851 domain, and both domains show low structural similarities to known structures. There is a positive groove mainly located in the GAD-like domain that may be associated with nucleotide binding. The structure provides a basis for further study of the positive groove as a potential active site.

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Organizational Affiliation: 

Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type VI immunity protein Atu4351	A	232	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu4351
UniProt
Find proteins for Q7CUQ2 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CUQ2  Go to UniProtKB:  Q7CUQ2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.250 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.445	α = 90
b = 92.445	β = 90
c = 86.157	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-26 
• Released Date: 2019-03-20 
Deposition Author(s): Shi, L., Gao, Z., Zhang, H., Dong, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670059

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release