2CS7 | pdb_00002cs7

1.2 A Crystal structure of the S. pneumoniae PhtA histidine triad domain a novel zinc binding fold

• PDB DOI: https://doi.org/10.2210/pdb2CS7/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-05-20 Released: 2006-02-14 
• Deposition Author(s): Riboldi-Tunnicliffe, A., Isaacs, N.W., Mitchell, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.135 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.112 (Depositor), 0.113 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Literature

1.2 Angstroms crystal structure of the S. pneumoniae PhtA histidine triad domain a novel zinc binding fold.

Riboldi-Tunnicliffe, A., Isaacs, N.W., Mitchell, T.J.

(2005) FEBS Lett 579: 5353-5360

• PubMed: 16194532 
• DOI: https://doi.org/10.1016/j.febslet.2005.08.066
• Primary Citation Related Structures: 
  2CS7


• PubMed Abstract: 
  

  The recently described pneumococcal histidine triad protein family has been shown to be highly conserved within the pneumococcus. As part of our structural genomics effort on proteins from Streptococcus pneumoniae, we have expressed, crystallised and solved the structure of PhtA-166-220 at 1.2 Angstroms using remote SAD with zinc. The structure of PhtA-166-220 shows no similarity to any protein structure. The overall fold contains 3beta-strands and a single short alpha-helix. The structure appears to contain a novel zinc binding motif. The remaining 4 histidine triad repeats from PhtA have been modelled based on the crystal structure of the PhtA histidine triad repeat 2. From this modelling work, we speculate that only three of the five histidine triad repeats contain the residues in the correct geometry to allow the binding of a zinc ion.

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Organizational Affiliation: 
• University of Glasgow, Division of Infection and Immunity, IBLS Joseph Black Building, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.27 kDa 
• Atom Count: 1,493 
• Modeled Residue Count: 164 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pneumococcal histidine triad A protein	A, B, C	55	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: PhtA (18-220)
UniProt
Find proteins for A0A0H2UQ89 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQ89  Go to UniProtKB:  A0A0H2UQ89

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.135 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.112 (Depositor), 0.113 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.182	α = 90
b = 35.895	β = 90.01
c = 72.541	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Riboldi-Tunnicliffe, A., Isaacs, N.W., Mitchell, T.J.

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations