6PON | pdb_00006pon

CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF FIBRONECTIN- BINDING PROTEIN PAVA FROM STREPTOCOCCUS PNEUMONIAE

• PDB DOI: https://doi.org/10.2210/pdb6PON/pdb

• Classification: CELL ADHESION
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-04 Released: 2019-07-31 
• Deposition Author(s): Manne, K., Narayana, S.V.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.237 (Depositor) 
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the N-terminal domain of the fibronectin-binding protein PavA from Streptococcus pneumoniae.

Manne, K., Narayana, S.V.L., Chattopadhyay, D.

(2019) Acta Crystallogr F Struct Biol Commun 75: 657-662

• PubMed: 31584015 
• DOI: https://doi.org/10.1107/S2053230X19012160
• Primary Citation of Related Structures:  
  6PON


• PubMed Abstract: 
  

  The Gram-positive bacterium Streptococcus pneumoniae, a major human pathogen, is a regular colonizer of the upper and lower respiratory tracts. Pneumococcal adherence and virulence factor A (PavA), a fibronectin-binding bacterial protein, from S. pneumoniae is an important facilitator of its colonization of host cells. In this study, the crystal structure of the N-terminal domain of PavA (SpPavA-N) determined at a resolution of 2.39 Å is reported. Each monomer of the dimeric protein consists of two domains (domains I and II) and a short α-helix (α6) at the C-terminus that are connected by elongated loops. Comparison of the SpPavA-N structure with that of its homolog from Streptococcus suis (FBPS-N) revealed differences in α5, α6 and the domain II/α6 inter-loop region within domain II. The α5 helix of FBPS-N folds back toward domain I, whereas in SpPavA-N it adopts an elongated rod shape.

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Organizational Affiliation: 
• Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.9 kDa 
• Atom Count: 4,555 
• Modeled Residue Count: 520 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adherence and virulence protein A	A, B	274	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: pavA
UniProt
Find proteins for Q8DQ36 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DQ36  Go to UniProtKB:  Q8DQ36

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.237 (Depositor) 
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.873	α = 90
b = 46.814	β = 90.931
c = 83.678	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Currently 6PON does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Manne, K., Narayana, S.V.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01- AI106808

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2019-09-04
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2019-10-16
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description