6CSL

Pneumococcal PhtD protein 269-339 fragment with bound Zn(II)

• PDB DOI: https://doi.org/10.2210/pdb6CSL/pdb

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


• Deposited: 2018-03-20 Released: 2018-06-13 
• Deposition Author(s): Luo, Z., Pederick, V.G., Paton, J.C., McDevitt, C.A., Kobe, B.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.198 
• R-Value Work: 0.148 
• R-Value Observed: 0.153 

Literature

Structural characterisation of the HT3 motif of the polyhistidine triad protein D from Streptococcus pneumoniae.

Luo, Z., Pederick, V.G., Paton, J.C., McDevitt, C.A., Kobe, B.

(2018) FEBS Lett 592: 2341-2350

• PubMed: 29856892 
• DOI: https://doi.org/10.1002/1873-3468.13122
• Primary Citation of Related Structures:  
  6CSL


• PubMed Abstract: 
  

  The bacterium Streptococcus pneumoniae (the pneumococcus) is a major human pathogen that requires Zn ²⁺ for its survival and virulence in the host environment. Polyhistidine triad protein D (PhtD) has a known role in pneumococcal Zn ²⁺ homeostasis. However, the mechanistic basis of PhtD function remains unclear, partly due to a lack of structural information. Here, we determined the crystal structure of the fragment PhtD ^269-339 , containing the third Zn ²⁺ -binding histidine triad (HT) motif of the protein. Analysis of the structure suggests that Zn ²⁺ binding occurs at the surface of the protein and that all five HT motifs in the protein bind Zn ²⁺ and share similar structures. These new structural insights aid in our understanding of how the Pht proteins facilitate pneumococcal Zn ²⁺ acquisition.

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Organizational Affiliation: 

School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 8.01 kDa 
• Atom Count: 632 
• Modelled Residue Count: 71 
• Deposited Residue Count: 71 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad protein D	A	71	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: phtD
UniProt
Find proteins for Q8DQ08 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DQ08  Go to UniProtKB:  Q8DQ08

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.198 
• R-Value Work: 0.148 
• R-Value Observed: 0.153 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.034	α = 90
b = 47.978	β = 107.13
c = 23.595	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Luo, Z., Pederick, V.G., Paton, J.C., McDevitt, C.A., Kobe, B.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1071659
National Health and Medical Research Council (NHMRC, Australia)	Australia	1080784
National Health and Medical Research Council (NHMRC, Australia)	Australia	1122582
Australian Research Council (ARC)	Australia	DP150104515
Australian Research Council (ARC)	Australia	DP170102102

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references