2XGA | pdb_00002xga

MTSL spin-labelled Shigella Flexneri Spa15

• PDB DOI: https://doi.org/10.2210/pdb2XGA/pdb

• Classification: CHAPERONE
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-02 Released: 2010-12-01 
• Deposition Author(s): Lillington, J.E.D., Johnson, S., Lea, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.264 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Shigella Flexneri Spa15 Crystal Structure Verified in Solution by Double Electron Electron Resonance.

Lillington, J.E.D., Lovett, J.E., Johnson, S., Roversi, P., Timmel, C.R., Lea, S.M.

(2011) J Mol Biology 405: 427

• PubMed: 21075116 
• DOI: https://doi.org/10.1016/j.jmb.2010.10.053
• Primary Citation Related Structures: 
  2XGA


• PubMed Abstract: 
  

  Shigella flexneri Spa15 is a chaperone of the type 3 secretion system, which binds a number of effectors to ensure their stabilization prior to secretion. One of these effectors is IpgB1, a mimic of the human Ras-like Rho guanosine triphosphatase RhoG. In this study, Spa15 alone and in complex with IpgB1 has been studied by double electron electron resonance, an experiment that gives distance information showing the spacial separation of attached spin labels. This distance is explained by determining the crystal structure of the spin-labeled Spa15 where labels are seen to be buried in hydrophobic pockets. The double electron electron resonance experiment on the Spa15 complex with IpgB1 shows that IpgB1 does not bind Spa15 in the same way as is seen in the homologous Salmonella sp. chaperone:effector complex InvB:SipA.

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Organizational Affiliation: 
• Inorganic Chemistry Laboratory, University of Oxford, OX1 3QR, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.12 kDa 
• Atom Count: 2,156 
• Modeled Residue Count: 255 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAK	A, B	153	Shigella flexneri	Mutation(s): 0
UniProt
Find proteins for P35530 (Shigella flexneri) Explore P35530  Go to UniProtKB:  P35530

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTN	C [auth A], D [auth B]	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate C10 H18 N O3 S2 MXZPGYFBZHBAQM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.264 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.98	α = 90
b = 50.38	β = 117.03
c = 57.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Lillington, J.E.D., Johnson, S., Lea, S.M.

Revision History  

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-05-12
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary