4QQA | pdb_00004qqa

Crystal structure of pneumolysin from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb4QQA/pdb

Classification: TOXIN
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-27 Released: 2015-08-05
Deposition Author(s): Park, S.A., Lee, K.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of pneumolysin from Streptococcus pneumoniae

Park, S.A., Lee, K.S.

To be published.

Macromolecule Content

Total Structure Weight: 54.35 kDa
Atom Count: 3,968
Modeled Residue Count: 483
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pneumolysin	A	484	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: ply
UniProt
Find proteins for Q2XU26 (Streptococcus pneumoniae) Explore Q2XU26 Go to UniProtKB: Q2XU26
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2XU26
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.722	α = 90
b = 159.931	β = 90
c = 209.358	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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.