3AK8 | pdb_00003ak8

Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis

• PDB DOI: https://doi.org/10.2210/pdb3AK8/pdb

• Classification: METAL BINDING PROTEIN, Oxidoreductase
• Organism(s): Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-08 Released: 2011-01-12 
• Deposition Author(s): Miyamoto, T., Asahina, Y., Miyazaki, S., Shimizu, H., Ohto, U., Noguchi, S., Satow, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.212 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structures of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis

Miyamoto, T., Asahina, Y., Miyazaki, S., Shimizu, H., Ohto, U., Noguchi, S., Satow, Y.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 17-22

• PubMed: 21206015 
• DOI: https://doi.org/10.1107/S1744309110043113
• Primary Citation Related Structures: 
  3AK8, 3AK9


• PubMed Abstract: 
  

  The crystal structure of SEp22, a DNA-binding protein from starved cells from Salmonella enterica subsp. enterica serovar Enteritidis, has been determined in two forms: the native state at 1.25 Å resolution and an iron-soaked form at 1.30 Å resolution. The SEp22 protomers form a dodecameric shell with 23 symmetry and a single iron ion per protomer was found at the ferroxidase centre in the iron-soaked form. Along the threefold axes of the 23 symmetry, hydrophilic Asp channels that consist of Asp146 were found. Iron ions may flow into the cavity of the dodecameric shell through the Asp channels.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, Japan.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 225.85 kDa 
• Atom Count: 16,657 
• Modeled Residue Count: 1,863 
• Deposited Residue Count: 2,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA protection during starvation protein	A, B, C, D, E, F, G, H, I, J, K, L	167	Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188	Mutation(s): 0  EC: 1.16

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	BA [auth I], FA [auth L], M [auth A], Q [auth B], W [auth F], Y [auth G]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	AA [auth H], CA [auth I], DA [auth I], EA [auth K], GA [auth L], N [auth A], O [auth A], P [auth A], R [auth B], S [auth B], T [auth B], U [auth C], V [auth D], X [auth F], Z [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.212 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.699	α = 90
b = 98.383	β = 90
c = 208.915	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): Miyamoto, T., Asahina, Y., Miyazaki, S., Shimizu, H., Ohto, U., Noguchi, S., Satow, Y.

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description