Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39010.79 
• Atom Count: 2550 
• Residue Count: 359 
• Unique protein chains: 1

1N67

Clumping Factor A from Staphylococcus aureus

• DOI: 10.2210/pdb1N67/pdb

• Classification: CELL ADHESION
• Organism(s): Staphylococcus aureus (strain Newman)
• Expression System: Escherichia coli


• 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: 1.9 Å
• R-Value Free: 0.256 
• R-Value Work: 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 


• 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

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.256 
• R-Value Work: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 38.700	α = 90.00
b = 80.540	β = 90.00
c = 113.890	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
SOLVE	phasing

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description
• Version 1.4: 2018-01-31
  Type: Experimental preparation