2XJN

Crystal structure of Streptococcus suis Dpr with copper


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Thermodynamic Characterization of Metal Ion Binding in Streptococcus Suis Dpr.

Haikarainen, T.Thanassoulas, A.Stavros, P.Nounesis, G.Haataja, S.Papageorgiou, A.C.

(2011) J Mol Biol 405: 448

  • DOI: https://doi.org/10.1016/j.jmb.2010.10.058
  • Primary Citation of Related Structures:  
    2XJM, 2XJN, 2XJO, 2XKQ

  • PubMed Abstract: 

    The use of protein cages for the creation of novel inorganic nanomaterials has attracted considerable attention in recent years. Ferritins are among the most commonly used protein cages in nanoscience. Accordingly, the binding of various metals to ferritins has been studied extensively. Dps (DNA-binding protein from starved cells)-like proteins belong to the ferritin superfamily. In contrast to ferritins, Dps-like proteins form 12-mers instead of 24-mers, have a different ferroxidase center, and are able to store a smaller amount of iron atoms in a hollow cavity (up to ∼500, instead of the ∼4500 iron atoms found in ferritins). With the exception of iron, the binding of other metal cations to Dps proteins has not been studied in detail. Here, the binding of six divalent metal ions (Zn(2+), Mn(2+), Ni(2+), Co(2+), Cu(2+), and Mg(2+)) to Streptococcus suisDps-like peroxide resistance protein (SsDpr) was characterized by X-ray crystallography and isothermal titration calorimetry (ITC). All metal cations, except for Mg(2+), were found to bind to the ferroxidase center similarly to Fe(2+), with moderate affinity (binding constants between 0.1×10(5) M(-1) and 5×10(5) M(-1)). The stoichiometry of binding, as deduced by ITC data, suggested the presence of a dication ferroxidase site. No other metal binding sites were identified in the protein. The results presented here demonstrate the ability of SsDpr to bind various metals as substitutes for iron and will help in better understanding protein-metal interactions in the Dps family of proteins as potential metal nanocontainers.


  • Organizational Affiliation

    Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku 20521, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA PROTECTION DURING STARVATION PROTEIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
165Streptococcus suisMutation(s): 0 
EC: 1.16
UniProt
Find proteins for P0CB53 (Streptococcus suis)
Explore P0CB53 
Go to UniProtKB:  P0CB53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CB53
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
CA [auth I],
IA [auth K],
O [auth B],
T [auth E]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
DA [auth I]
GA [auth J]
JA [auth K]
KA [auth L]
M [auth A]
DA [auth I],
GA [auth J],
JA [auth K],
KA [auth L],
M [auth A],
P [auth B],
Q [auth C],
R [auth D],
U [auth E],
V [auth F],
Y [auth G],
Z [auth H]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth H],
FA [auth I],
HA [auth J],
LA [auth L],
W [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth H],
EA [auth I],
N [auth A],
S [auth D],
X [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.84α = 90
b = 137.71β = 90
c = 142.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection