1H8G | pdb_00001h8g

C-terminal domain of the major autolysin (C-LytA) from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb1H8G/pdb

• Classification: CHOLINE-BINDING DOMAIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2001-02-06 Released: 2002-01-31 
• Deposition Author(s): Fernandez-Tornero, C., Garcia, E., Lopez, R., Gimenez-Gallego, G., Romero, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factor Lyta

Fernandez-Tornero, C., Lopez, R., Garcia, E., Gimenez-Gallego, G., Romero, A.

(2001) Nat Struct Biol 8: 1020

• PubMed: 11694890 
• DOI: https://doi.org/10.1038/nsb724
• Primary Citation Related Structures: 
  1H8G, 1HCX


• PubMed Abstract: 
  

  Choline binding proteins are virulence determinants present in several Gram-positive bacteria. Because anchorage of these proteins to the cell wall through their choline binding domain is essential for bacterial virulence, their release from the cell surface is considered a powerful target for a weapon against these pathogens. The first crystal structure of a choline binding domain, from the toxin-releasing enzyme pneumococcal major autolysin (LytA), reveals a novel solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix. This unique structure is maintained by choline molecules at the hydrophobic interface of consecutive hairpins and may be present in other choline binding proteins that share high homology to the repeated motif of the domain.

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Organizational Affiliation: 
• Departamento de Estructura y Función de Proteínas, Centro de Investigaciones Biológicas - CSIC, C/ Velázquez 144, Madrid, 28006, Spain.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 22.93 kDa 
• Atom Count: 1,655 
• Modeled Residue Count: 189 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR AUTOLYSIN	A, B	95	Streptococcus pneumoniae	Mutation(s): 3  Gene Names: LYTA EC: 3.5.1.28
UniProt
Find proteins for P06653 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P06653  Go to UniProtKB:  P06653

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CHT	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	CHOLINE ION C5 H14 N O OEYIOHPDSNJKLS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.571	α = 90
b = 97.571	β = 90
c = 68.482	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-31 
Deposition Author(s): Fernandez-Tornero, C., Garcia, E., Lopez, R., Gimenez-Gallego, G., Romero, A.

Revision History  

• Version 1.0: 2002-01-31
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary