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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.277 (Depositor), 0.281 (DCC)
R-Value Work:
0.218 (Depositor), 0.224 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Wild Type Pneumolysin

Van Pee, K., Yildiz, O.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7ZAK5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.277 (Depositor), 0.281 (DCC)
R-Value Work: 0.218 (Depositor), 0.224 (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

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.