5AOD | pdb_00005aod

Crystal structure of wild type pneumolysin.

• PDB DOI: https://doi.org/10.2210/pdb5AOD/pdb

• Classification: TOXIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2015-09-10 Released: 2016-10-05 
• Deposition Author(s): van Pee, K., Yildiz, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Wild Type Pneumolysin

Van Pee, K., Yildiz, O.

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: 53.24 kDa 
• Atom Count: 3,777 
• Modeled Residue Count: 474 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PNEUMOLYSIN	A	474	Streptococcus pneumoniae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q7ZAK5 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q7ZAK5  Go to UniProtKB:  Q7ZAK5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.28	α = 90
b = 113.26	β = 90
c = 156.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): van Pee, K., Yildiz, O.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description