5CYB

Structure of a lipocalin lipoprotein affecting virulence in Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb5CYB/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-30 Released: 2016-09-14 
• Deposition Author(s): Carrasco-Lopez, C., Abdullah, M.R., Hammerschmidt, S., Hermoso, J.A.
• Funding Organization(s): the Government of Community of Madrid, German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.217 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Unraveling the function and structure of a lipocalin lipoprotein affecting virulence in Streptococcus pneumoniae

Abdullah, M.R., Carrasco-Lopez, C., Saleh, M., Gomez, A., Petruschka, L., VoB, F., Pribyl, T., Hermoso, J.A., Hammerschmidt, S.

To be published.

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: 16.78 kDa 
• Atom Count: 779 
• Modelled Residue Count: 89 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein	A	152	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: ERS019416_00104, ERS019595_00220, ERS021447_05272, ERS022232_05596, ERS409134_00058, ERS409372_00175, ERS515225_00124

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.217 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.485	α = 90
b = 107.485	β = 90
c = 63.87	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Carrasco-Lopez, C., Abdullah, M.R., Hammerschmidt, S., Hermoso, J.A.

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Funding Organization	Location	Grant Number
the Government of Community of Madrid	Spain	BFU2011-25326
German Research Foundation	Germany	1870, HA3125/4-2

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description