5I4J

Dps4 from Nostoc punctiforme in complex with Zn ions

• PDB DOI: https://doi.org/10.2210/pdb5I4J/pdb

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


• Deposited: 2016-02-12 Released: 2017-02-01 
• Deposition Author(s): Howe, C., Moparthi, V.K., Persson, K., Stensjo, K.
• Funding Organization(s): Swedish Energy Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.214 (Depositor) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

On the trail of iron into Dps4 from N. punctiforme

Howe, C., Moparthi, V.K., Persson, K., Stensjo, K.

To be published.

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: 80.56 kDa 
• Atom Count: 5,742 
• Modelled Residue Count: 708 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin, Dps family protein	A, B, C, D	177	Nostoc punctiforme	Mutation(s): 0  Gene Names: Npun_R5799
UniProt
Find proteins for B2J981 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J981  Go to UniProtKB:  B2J981

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN	E [auth A], G [auth A], H [auth C], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.214 (Depositor) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.92	α = 90
b = 100.92	β = 90
c = 144.27	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Howe, C., Moparthi, V.K., Persson, K., Stensjo, K.

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Funding Organization	Location	Grant Number
Swedish Energy Agency	Sweden	11674-5

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description