2VVZ

Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

Structure of the Catalytic Domain of Streptococcus Pneumoniae Sialidase Nana.

Xu, G.Li, X.Andrew, P.W.Taylor, G.L.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 772

  • DOI: https://doi.org/10.1107/S1744309108024044
  • Primary Citation of Related Structures:  
    2VVZ, 2W20

  • PubMed Abstract: 

    Streptococcus pneumoniae genomes encode three sialidases, NanA, NanB and NanC, which are key virulence factors that remove sialic acids from various glycoconjugates. The enzymes have potential as drug targets and also as vaccine candidates. The 115 kDa NanA is the largest of the three sialidases and is anchored to the bacterial membrane. Although recombinantly expressed full-length NanA was soluble, it failed to crystallize; therefore, a 56.5 kDa domain that retained full enzyme activity was subcloned. The purified enzyme was crystallized in 0.1 M MES pH 6.5, 30%(w/v) PEG 4000 using the sitting-drop vapour-diffusion method. Data were collected at 100 K to 2.5 A resolution from a crystal grown in the presence of the inhibitor 2-deoxy-2,3-dehydro-N-acetyl neuraminic acid. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 49.2, b = 95.6, c = 226.6 A. The structure was solved by molecular replacement and refined to final R and R(free) factors of 0.246 and 0.298, respectively.


  • Organizational Affiliation

    Centre for Biomolecular Sciences, University of St Andrews, St Andrews, Fife KY16 9ST, Scotland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIALIDASE A
A, B
504Streptococcus pneumoniaeMutation(s): 0 
EC: 3.2.1.18
UniProt
Find proteins for P62575 (Streptococcus pneumoniae)
Explore P62575 
Go to UniProtKB:  P62575
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62575
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DAN BindingDB:  2VVZ Ki: 1600 (nM) from 1 assay(s)
IC50: min: 4800, max: 1.00e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.206α = 90
b = 95.626β = 90
c = 226.596γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other
  • Version 1.5: 2020-09-02
    Changes: Derived calculations, Structure summary
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Refinement description