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.

Macromolecule Content

• Total Structure Weight: 39.01 kDa 
• Atom Count: 2926 
• Modelled Residue Count: 332 
• Deposited Residue Count: 359 
• Unique protein chains: 1

1N67

Clumping Factor A from Staphylococcus aureus

• PDB DOI: 10.2210/pdb1N67/pdb

• Classification: CELL ADHESION
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-11-08 Released: 2003-03-04 
• Deposition Author(s): Deivanayagam, C.C.S., Wann, E.R., Chen, W., Carson, M., Rajashankar, K.R., Hook, M., Narayana, S.V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor A

Deivanayagam, C.C.S., Wann, E.R., Chen, W., Carson, M., Rajashankar, K.R., Hook, M., Narayana, S.V.L.

(2002) EMBO J 21: 6660-6672

• PubMed: 12485987 
• DOI: 10.1093/emboj/cdf619
• Primary Citation of Related Structures:  
  1N67


• PubMed Abstract: 
  

We report here the crystal structure of the minimal ligand-binding segment of the Staphylococcus aureus MSCRAMM, clumping factor A. This fibrinogen-binding segment contains two similarly folded domains. The fold observed is a new variant of the immunoglobulin motif that we have called DE-variant or the DEv-IgG fold. This subgroup includes the ligand-binding domain of the collagen-binding S.aureus MSCRAMM CNA, and many other structures previously classified as jelly rolls. Structure predictions suggest that the four fibrinogen-binding S.aureus MSCRAMMs identified so far would also contain the same DEv-IgG fold. A systematic docking search using the C-terminal region of the fibrinogen gamma-chain as a probe suggested that a hydrophobic pocket formed between the two DEv-IgG domains of the clumping factor as the ligand-binding site. Mutagenic substitution of residues Tyr256, Pro336, Tyr338 and Lys389 in the clumping factor, which are proposed to contact the terminal residues (408)AGDV(411) of the gamma-chain, resulted in proteins with no or markedly reduced affinity for fibrinogen.

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Organizational Affiliation: 

Center for Biophysical Sciences and Engineering, School of Optometry, 244 CBSE, 1025 18th Street South, University of Alabama at Birmingham, Birmingham, AL 35294-0005, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clumping Factor	A	359	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q53653 (Staphylococcus aureus (strain Newman)) Explore Q53653  Go to UniProtKB:  Q53653

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.7	α = 90
b = 80.54	β = 90
c = 113.89	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-08 
• Released Date: 2003-03-04 
Deposition Author(s): Deivanayagam, C.C.S., Wann, E.R., Chen, W., Carson, M., Rajashankar, K.R., Hook, M., Narayana, S.V.L.

Revision History  

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-01-31
  Changes: Experimental preparation