5MLT | pdb_00005mlt

Structural characterization of a carbohydrate substrate binding protein from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb5MLT/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-07 Released: 2017-01-11 
• Deposition Author(s): Culurgioni, S., Tang, M., Walsh, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.229 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Structural characterization of the Streptococcus pneumoniae carbohydrate substrate-binding protein SP0092.

Culurgioni, S., Tang, M., Walsh, M.A.

(2017) Acta Crystallogr F Struct Biol Commun 73: 54-61

• PubMed: 28045395 
• DOI: https://doi.org/10.1107/S2053230X16020252
• Primary Citation Related Structures: 
  5MLT


• PubMed Abstract: 
  

  Streptococcus pneumoniae is an opportunistic respiratory pathogen that remains a major cause of morbidity and mortality globally, with infants and the elderly at the highest risk. S. pneumoniae relies entirely on carbohydrates as a source of carbon and dedicates a third of all uptake systems to carbohydrate import. The structure of the carbohydrate-free substrate-binding protein SP0092 at 1.61 Å resolution reveals it to belong to the newly proposed subclass G of substrate-binding proteins, with a ligand-binding pocket that is large enough to accommodate complex oligosaccharides. SP0092 is a dimer in solution and the crystal structure reveals a domain-swapped dimer with the monomer subunits in a closed conformation but in the absence of carbohydrate ligand. This closed conformation may be induced by dimer formation and could be used as a mechanism to regulate carbohydrate uptake.

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Organizational Affiliation: 
• Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England.

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: 51.47 kDa 
• Atom Count: 3,945 
• Modeled Residue Count: 454 
• Deposited Residue Count: 455 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, substrate-binding protein	A	455	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: SP_0092
UniProt
Find proteins for A0A0H2UMY0 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UMY0  Go to UniProtKB:  A0A0H2UMY0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.229 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.24	α = 90
b = 82.54	β = 107.76
c = 60.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
SHELXCD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Culurgioni, S., Tang, M., Walsh, M.A.

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary