Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 6.83 kDa 
• Atom Count: 984 
• Modelled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique protein chains: 1

4NPD

High-resolution structure of C domain of staphylococcal protein A at cryogenic temperature

• PDB DOI: 10.2210/pdb4NPD/pdb

• Classification: PROTEIN BINDING
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-21 Released: 2014-10-08 
• Deposition Author(s): Deis, L.N., Pemble IV, C.W., Oas, T.G., Richardson, J.S., Richardson, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 0.130 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 

Literature

Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity.

Deis, L.N., Pemble, C.W., Qi, Y., Hagarman, A., Richardson, D.C., Richardson, J.S., Oas, T.G.

(2014) Structure 22: 1467-1477

• PubMed: 25295398 
• DOI: 10.1016/j.str.2014.08.014
• Primary Citation of Related Structures:  
  4NPD, 4NPE, 4NPF


• PubMed Abstract: 
  

The Staphylococcus aureus virulence factor staphylococcal protein A (SpA) is a major contributor to bacterial evasion of the host immune system, through high-affinity binding to host proteins such as antibodies. SpA includes five small three-helix-bundle domains (E-D-A-B-C) separated by conserved flexible linkers. Prior attempts to crystallize individual domains in the absence of a binding partner have apparently been unsuccessful. There have also been no previous structures of tandem domains. Here we report the high-resolution crystal structures of a single C domain, and of two B domains connected by the conserved linker. Both structures exhibit extensive multiscale conformational heterogeneity, which required novel modeling protocols. Comparison of domain structures shows that helix1 orientation is especially heterogeneous, coordinated with changes in side chain conformational networks and contacting protein interfaces. This represents the kind of structural plasticity that could enable SpA to bind multiple partners.

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Organizational Affiliation: 

Department of Biochemistry, Duke University, Durham, NC 27710, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein A	A	58	Staphylococcus aureus	Mutation(s): 0  Gene Names: protein A, spa
UniProt
Find proteins for P38507 (Staphylococcus aureus) Explore P38507  Go to UniProtKB:  P38507

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN	D [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 0.130 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.25	α = 90
b = 38.41	β = 117.44
c = 28.61	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-11-21 
• Released Date: 2014-10-08 
Deposition Author(s): Deis, L.N., Pemble IV, C.W., Oas, T.G., Richardson, J.S., Richardson, D.C.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description