4WK1 | pdb_00004wk1

Crystal structure of Staphylococcus aureus PstA in complex with c-di-AMP

• PDB DOI: https://doi.org/10.2210/pdb4WK1/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-01 Released: 2014-11-26 
• Deposition Author(s): Mueller, M., Hopfner, K.-P., Witte, G.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.229 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

c-di-AMP recognition by Staphylococcus aureus PstA.

Muller, M., Hopfner, K., Witte, G.

(2015) FEBS Lett 589: 45-51

• PubMed: 25435171 
• DOI: https://doi.org/10.1016/j.febslet.2014.11.022
• Primary Citation Related Structures: 
  4WK1, 4WK3


• PubMed Abstract: 
  

  Cyclic-di-AMP (c-di-AMP) is a bacterial secondary messenger involved in various processes, including sensing of DNA-integrity, cell wall metabolism and potassium transport. A number of c-di-AMP receptor proteins have recently been identified in Staphylococcus aureus. One of them - PstA - possesses a ferredoxin-like fold and is structurally related to the class of PII signal-transduction proteins. PII proteins are involved in a large number of pathways, most of them associated with nitrogen metabolism. In this study we describe the mode of c-di-AMP binding and subsequent structural changes of S. aureus PstA. An altered architecture in PstA compared to canonical PII proteins results in differences in ligand coordination.

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Organizational Affiliation: 
• Ludwig-Maximilians-Universität München, Gene Center and Dept. of Biochemistry, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
Ludwig-Maximilians-Universität München, Gene Center and Dept. of Biochemistry, Feodor-Lynen-Str. 25, 81377 Munich, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 14.72 kDa 
• Atom Count: 773 
• Modeled Residue Count: 92 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PstA	A	129	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: SACOL0525
UniProt
Find proteins for A0A0H2WXZ7 (Staphylococcus aureus (strain COL)) Explore A0A0H2WXZ7  Go to UniProtKB:  A0A0H2WXZ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BA	B [auth A]	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide C20 H24 N10 O12 P2 PDXMFTWFFKBFIN-XPWFQUROSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.229 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.1	α = 90
b = 68.1	β = 90
c = 135.74	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Mueller, M., Hopfner, K.-P., Witte, G.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	3717/2-1
German Research Foundation	Germany	GRK1721

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2014-12-31
  Changes: Database references
• Version 2.0: 2024-01-10
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary