1ATG

AZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE-BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.164 

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This is version 1.3 of the entry. See complete history


Literature

Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.

Lawson, D.M.Williams, C.E.Mitchenall, L.A.Pau, R.N.

(1998) Structure 6: 1529-1539

  • DOI: https://doi.org/10.1016/s0969-2126(98)00151-8
  • Primary Citation of Related Structures:  
    1ATG

  • PubMed Abstract: 

    . Periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. Nevertheless, almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains. The ligand is bound at the bottom of a deep cleft, which lies at the interface between these two domains. The oxyanion-binding proteins are notable in that they can discriminate between very similar ligands. . Azotobacter vinelandii is unusual in that it possesses two periplasmic molybdate-binding proteins. The crystal structure of one of these with bound ligand has been determined at 1.2 A resolution. It superficially resembles the structure of sulphate-binding protein (SBP) from Salmonella typhimurium and uses a similar constellation of hydrogen-bonding interactions to bind its ligand. However, the detailed interactions are distinct from those of SBP and the more closely related molybdate-binding protein of Escherichia coli. . Despite differences in the residues involved in binding, the volumes of the binding pockets in the A. vinelandii and E. coli molybdate-binding proteins are similar and are significantly larger than that of SBP. We conclude that the discrimination between molybdate and sulphate shown by these binding proteins is largely dependent upon small differences in the sizes of these two oxyanions.


  • Organizational Affiliation

    Nitrogen Fixation Laboratory John Innes Centre Norwich NR4 7UH UK. david.lawson@bbsrc.ac.uk


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC MOLYBDATE-BINDING PROTEIN231Azotobacter vinelandiiMutation(s): 0 
UniProt
Find proteins for Q7SIH2 (Azotobacter vinelandii)
Explore Q7SIH2 
Go to UniProtKB:  Q7SIH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIH2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.934α = 90
b = 88.802β = 93.55
c = 41.746γ = 90
Software Package:
Software NamePurpose
VARIOUSmodel building
DMmodel building
Omodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
DMphasing
OTHERS)phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations