5HJF

The apo form of Dps4 from Nostoc punctiforme

• PDB DOI: https://doi.org/10.2210/pdb5HJF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Nostoc punctiforme
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2016-01-13 Released: 2017-01-25 
• 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: 1.59 Å
• R-Value Free: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Literature

On the trail of iron and zinc bindning to 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: 83.79 kDa 
• Atom Count: 6,517 
• Modelled Residue Count: 722 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin, Dps family protein	A, B, C, D	185	Nostoc punctiforme	Mutation(s): 1  Gene Names: Npun_R5799
UniProt
Find proteins for B2J981 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J981  Go to UniProtKB:  B2J981

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.884	α = 90
b = 101.884	β = 90
c = 146.25	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-25 
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: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references