2JH3

The crystal structure of DR2241 from Deinococcus radiodurans at 1.9 A resolution reveals a multi-domain protein with structural similarity to chelatases but also with two additional novel domains

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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This is version 1.2 of the entry. See complete history. 


Literature

The Crystal Structure of Dr2241 from Deinococcus Radiodurans at 1.9 A Resolution Reveals a Multi-Domain Protein with Structural Similarity to Chelatases But Also with Two Additional Novel Domains

Leiros, H.-K.S., Mcsweeney, S.M.

(2007) J Struct Biol 159: 92

  • DOI: 10.1016/j.jsb.2007.02.009
  • Primary Citation of Related Structures:  
    2JH3

  • PubMed Abstract: 

    • A unique family of proteins have been identified in the Deinococcus genus with an N-terminal cobalamin (vitamin B(12)) chelatase domain denoted CbiX and an additional unique C-terminal domain with unknown function. Here we report the first crystal structure from this new family of proteins with the structure of Deinococcus radiodurans protein DR2241 ...

    A unique family of proteins have been identified in the Deinococcus genus with an N-terminal cobalamin (vitamin B(12)) chelatase domain denoted CbiX and an additional unique C-terminal domain with unknown function. Here we report the first crystal structure from this new family of proteins with the structure of Deinococcus radiodurans protein DR2241. The structure reveals a multi-domain protein where domains A (residues 1-132) has the same fold as the small CbiX (CbiX(S)), domains A and B (residues 1-272) follow the chelatase super-family fold and the two additional unique domains C and D have no structural homologues. Domain D harbours the sequence motifs CxxC and CxxxC, in which DR2241 gives the first evidence that these motifs bind a [4Fe-4S] iron-sulphur cluster. In solution there are indications of multimeric forms, and in the crystallographic asymmetric unit a tetramer is found where domains C and D are involved in stabilising the tetrameric assembly.

    Organizational Affiliation: 

    Macromolecular Crystallography Group, European Synchrotron Radiation Facility (ESRF), BP 220, 6, Rue Jules Horowitz, F-38043 Grenoble Cedex 09, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S2-RELATED PROTEINA, B, C, D474Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RS86 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RS86 
Go to UniProtKB:  Q9RS86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RS86
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.78α = 90
b = 128.69β = 90
c = 135.08γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
SHARPphasing
SOLVEphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance