3HIA | pdb_00003hia

Crystal structure of the choline binding domain of Spr1274 in Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb3HIA/pdb

• Classification: CHOLINE-BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-19 Released: 2009-08-04 
• Deposition Author(s): Zhang, Z.-Y., Li, W.-Z., Jiang, Y.-L., Bao, R., Zhou, C.-Z., Chen, Y.-X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.265 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Structure of the choline-binding domain of Spr1274 in Streptococcus pneumoniae.

Zhang, Z., Li, W., Frolet, C., Bao, R., di Guilmi, A.M., Vernet, T., Chen, Y.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 757-761

• PubMed: 19652332 
• DOI: https://doi.org/10.1107/S1744309109025329
• Primary Citation of Related Structures:  
  3HIA


• PubMed Abstract: 
  

  Spr1274 is a putative choline-binding protein that is bound to the cell wall of Streptococcus pneumoniae through noncovalent interactions with the choline moieties of teichoic and lipoteichoic acids. Its function is still unknown. The crystal structure of the choline-binding domain of Spr1274 (residues 44-129) was solved at 2.38 A resolution with three molecules in the asymmetric unit. It may provide a structural basis for functional analysis of choline-binding proteins.

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Organizational Affiliation: 
• Protein Research Institute, Tongji University, Shanghai 200092, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.06 kDa 
• Atom Count: 1,973 
• Modeled Residue Count: 223 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline binding protein	A, B, C	94	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: spr1274
UniProt
Find proteins for Q8DP99 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DP99  Go to UniProtKB:  Q8DP99

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC	D [auth A], F [auth B], G [auth B], H [auth B], I [auth B], K [auth C], L [auth C]	PHOSPHOCHOLINE C5 H15 N O4 P YHHSONZFOIEMCP-UHFFFAOYSA-O
SO4	E [auth A], J [auth B], M [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.265 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.61	α = 90
b = 140.61	β = 90
c = 46.05	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Zhang, Z.-Y., Li, W.-Z., Jiang, Y.-L., Bao, R., Zhou, C.-Z., Chen, Y.-X.

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-05-07
  Changes: Database references, Structure summary