8QJA

T6SS-linked Rhs repeat protein - Advenella mimigardefordensis VgrG-Rhs core

• PDB DOI: https://doi.org/10.2210/pdb8QJA/pdb

• Classification: CELL INVASION
• Organism(s): Advenella mimigardefordensis DPN7
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2023-09-13 Released: 2024-09-25 
• Deposition Author(s): Kielkopf, C.S., Shneider, M.M., Leiman, P.G., Taylor, N.M.I.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.36 Å
• R-Value Free: 0.317 
• R-Value Work: 0.257 
• R-Value Observed: 0.260 

Starting Model: experimental

Literature

T6SS-associated Rhs proteins form toxin containers: Structural and functional insights into bacterial weaponry and self-protection

Kielkopf, C.S., Shneider, M.M., Leiman, P.G., Taylor, N.M.I.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 851.29 kDa 
• Atom Count: 33,470 
• Modelled Residue Count: 4,088 
• Deposited Residue Count: 7,516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative type VI secretion system YD repeat-containing Rhs element Vgr protein	A, B, C, D	1,879	Advenella mimigardefordensis DPN7	Mutation(s): 0  Gene Names: MIM_c35070
UniProt
Find proteins for W0PIA9 (Advenella mimigardefordensis (strain DSM 17166 / LMG 22922 / DPN7)) Explore W0PIA9  Go to UniProtKB:  W0PIA9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.36 Å
• R-Value Free: 0.317 
• R-Value Work: 0.257 
• R-Value Observed: 0.260 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.239	α = 85.69
b = 97.783	β = 89.99
c = 215.006	γ = 76.89

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
Coot	model building
BUSTER	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Kielkopf, C.S., Shneider, M.M., Leiman, P.G., Taylor, N.M.I.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_144243

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release