4QQQ

Crystal structure of pneumolysin from Streptococcus pneumoniae, in complex with mannose as a component of cell membrane

• PDB DOI: https://doi.org/10.2210/pdb4QQQ/pdb

• Classification: TOXIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2014-06-27 Released: 2015-07-22 
• Deposition Author(s): Park, S.A., Lee, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Crystal structure of pneumolysin from Streptococcus pneumoniae, in complex with mannose as a component of cell membrane

Park, S.A., Lee, K.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 54.71 kDa 
• Atom Count: 3,967 
• Modelled Residue Count: 483 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pneumolysin	A	484	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: ply Membrane Entity: Yes
UniProt
Find proteins for Q2XU26 (Streptococcus pneumoniae) Explore Q2XU26  Go to UniProtKB:  Q2XU26

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	B [auth A], C [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.679	α = 90
b = 157.454	β = 90
c = 211.325	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Park, S.A., Lee, K.S.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary