1JI5 | pdb_00001ji5

Dlp-1 from bacillus anthracis

• PDB DOI: https://doi.org/10.2210/pdb1JI5/pdb

• Classification: METAL TRANSPORT
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-06-29 Released: 2002-06-19 
• Deposition Author(s): Papinutto, E., Dundon, W.G., Pitulis, N., Battistutta, R., Montecucco, C., Zanotti, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.291 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Structure of two iron-binding proteins from Bacillus anthracis.

Papinutto, E., Dundon, W.G., Pitulis, N., Battistutta, R., Montecucco, C., Zanotti, G.

(2002) J Biological Chem 277: 15093-15098

• PubMed: 11836250 
• DOI: https://doi.org/10.1074/jbc.M112378200
• Primary Citation Related Structures: 
  1JI5, 1JIG


• PubMed Abstract: 
  

  Bacillus anthracis is currently under intense investigation due to its primary importance as a human pathogen. Particularly important is the development of novel anti-anthrax vaccines, devoid of the current side effects. A novel class of immunogenic bacterial proteins consists of dodecamers homologous to the DNA-binding protein of Escherichia coli (Dps). Two Dps homologous genes are present in the B. anthracis genome. The crystal structures of these two proteins (Dlp-1 and Dlp-2) have been determined and are presented here. They are sphere-like proteins with an internal cavity. We also show that they act as ferritins and are thus involved in iron uptake and regulation, a fundamental function during bacterial growth.

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Organizational Affiliation: 
• Dipartimento di Chimica Organica e Centro CNR Biopolimeri, Università di Padova, Via Marzolo 1, 35131 Padova, Italy.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 66.04 kDa 
• Atom Count: 4,773 
• Modeled Residue Count: 568 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dlp-1	A, B, C, D	142	Bacillus anthracis	Mutation(s): 0  Gene Names: dlp-1 EC: 1.16
UniProt
Find proteins for Q8RPQ2 (Bacillus anthracis) Explore Q8RPQ2  Go to UniProtKB:  Q8RPQ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	G [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
FE	E [auth A], F [auth B], H [auth C], I [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.291 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.224	α = 90
b = 89.224	β = 90
c = 210.165	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-19 
Deposition Author(s): Papinutto, E., Dundon, W.G., Pitulis, N., Battistutta, R., Montecucco, C., Zanotti, G.

Revision History  

• Version 1.0: 2002-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description