1D2O | pdb_00001d2o

CRYSTAL STRUCTURE OF A SINGLE B REPEAT UNIT (B1) OF COLLAGEN BINDING SURFACE PROTEIN (CNA) OF STAPHYLOCOCCUS AUREUS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.256 (Depositor) 
  • R-Value Work: 
    0.212 (Depositor) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1D2O

This is version 1.4 of the entry. See complete history

Literature

Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein.

Deivanayagam, C.C.Rich, R.L.Carson, M.Owens, R.T.Danthuluri, S.Bice, T.Hook, M.Narayana, S.V.

(2000) Structure 8: 67-78

  • DOI: https://doi.org/10.1016/s0969-2126(00)00081-2
  • Primary Citation Related Structures: 
    1D2O, 1D2P

  • PubMed Abstract: 

    [corrected] The Staphylococcus aureus collagen-binding protein Cna mediates bacterial adherence to collagen. The primary sequence of Cna has a non-repetitive collagen-binding A region, followed by the repetitive B region. The B region has one to four 23 kDa repeat units (B(1)-B(4)), depending on the strain of origin. The affinity of the A region for collagen is independent of the B region. However, the B repeat units have been suggested to serve as a 'stalk' that projects the A region from the bacterial surface and thus facilitate bacterial adherence to collagen. To understand the biological role of these B-region repeats we determined their three-dimensional structure. B(1) has two domains (D(1) and D(2)) placed side-by-side. D(1) and D(2) have similar secondary structure and exhibit a unique fold that resembles but is the inverse of the immunoglobulin-like (IgG-like) domains. Comparison with similar immunoglobulin superfamily (IgSF) structures shows novel packing arrangements between the D(1) and D(2) domains. In the B(1)B(2) crystal structure, an omission of a single glycine residue in the D(2)-D(3) linker loop, compared to the D(1)-D(2) and D(3)-D(4) linker loops, resulted in projection of the D(3) and D(4) in a spatially new orientation. We also present a model for B(1)B(2)B(3)B(4). The B region of the Cna collagen adhesin has a novel fold that is reminiscent of but is inverse in nature to the IgG fold. This B region assembly could effectively provide the needed flexibility and stability for presenting the ligand binding A region away from the bacterial cell surface.


  • Organizational Affiliation
    • Center for Macromolecular Crystallography, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294-0005, USA.

Macromolecule Content 

  • Total Structure Weight: 42.53 kDa 
  • Atom Count: 3,079 
  • Modeled Residue Count: 374 
  • Deposited Residue Count: 374 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COLLAGEN ADHESIN
A, B
187Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q53654 (Staphylococcus aureus)
Explore Q53654 
Go to UniProtKB:  Q53654
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53654
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.256 (Depositor) 
  • R-Value Work:  0.212 (Depositor) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.907α = 90
b = 101.538β = 90
c = 121γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PHASESphasing
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references