2DGJ

Crystal structure of EbhA (756-1003 domain) from Staphylococcus aureus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A helical string of alternately connected three-helix bundles for the cell wall-associated adhesion protein Ebh from Staphylococcus aureus

Tanaka, Y., Sakamoto, S., Kuroda, M., Goda, S., Gao, Y.-G., Tsumoto, K., Hiragi, Y., Yao, M., Watanabe, N., Ohta, T., Tanaka, I.

(2008) Structure 16: 488-496

  • DOI: 10.1016/j.str.2007.12.018
  • Primary Citation of Related Structures:  
    2DGJ

  • PubMed Abstract: 

    • The 1.1 MDa cell-wall-associated adhesion protein of staphylococci, Ebh, consists of several distinct regions, including a large central region with 52 imperfect repeats of 126 amino acid residues. We investigated the structure of this giant molecule ...

    The 1.1 MDa cell-wall-associated adhesion protein of staphylococci, Ebh, consists of several distinct regions, including a large central region with 52 imperfect repeats of 126 amino acid residues. We investigated the structure of this giant molecule by X-ray crystallography, circular dichroism (CD) spectrometry, and small-angle X-ray scattering (SAXS). The crystal structure of two repeats showed that each repeat consists of two distinct three-helix bundles, and two such repeats are connected along the long axis, resulting in a rod-like structure that is 120 A in length. CD and SAXS analyses of the samples with longer repeats suggested that each repeat has an identical structure, and that such repeats are connected tandemly to form a rod-like structure in solution, the length of which increased proportionately with the number of repeating units. On the basis of these results, it was proposed that Ebh is a 320 nm rod-like molecule with some plasticity at module junctions.

    Organizational Affiliation: 

    Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hypothetical protein ebhAA, B257Staphylococcus aureusMutation(s): 0 
Find proteins for Q931R6 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore Q931R6 
Go to UniProtKB:  Q931R6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACY
Query on ACY
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.265α = 90
b = 161.848β = 90
c = 133.366γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
OASISphasing
DMphasing
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance