3ONR

Crystal structure of the calcium chelating immunodominant antigen, calcium dodecin (Rv0379),from Mycobacterium tuberculosis with a novel calcium-binding site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium-binding site.

Arockiasamy, A., Aggarwal, A., Savva, C.G., Holzenburg, A., Sacchettini, J.C.

(2011) Protein Sci 20: 827-833

  • DOI: 10.1002/pro.607
  • Primary Citation of Related Structures:  
    3ONR

  • PubMed Abstract: 

    • In eukaryotes, calcium-binding proteins play a pivotal role in diverse cellular processes, and recent findings suggest similar roles for bacterial proteins at different stages in their life cycle. Here, we report the crystal structure of calcium dodecin, Rv0379, from Mycobacterium tuberculosis with a dodecameric oligomeric assembly and a unique calcium-binding motif ...

    In eukaryotes, calcium-binding proteins play a pivotal role in diverse cellular processes, and recent findings suggest similar roles for bacterial proteins at different stages in their life cycle. Here, we report the crystal structure of calcium dodecin, Rv0379, from Mycobacterium tuberculosis with a dodecameric oligomeric assembly and a unique calcium-binding motif. Structure and sequence analysis were used to identify orthologs of Rv0379 with different ligand-binding specificity.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN TRANSPORT PROTEIN SECE2
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
72Mycobacterium tuberculosisMutation(s): 2 
Gene Names: Rv0379, secE2
UniProt
Find proteins for Q6MX43 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore Q6MX43 
Go to UniProtKB:  Q6MX43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MX43
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT
Download Ideal Coordinates CCD File 
AA [auth I],
T [auth E],
V [auth F]		PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
CA [auth J],
DA [auth K],
EA [auth L],
N [auth A],
O [auth B],
CA [auth J],
DA [auth K],
EA [auth L],
N [auth A],
O [auth B],
P [auth C],
R [auth D],
S [auth E],
U [auth F],
X [auth G],
Y [auth H],
Z [auth I]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
BA [auth J],
M [auth A],
Q [auth D],
W [auth G]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.193α = 90
b = 78.446β = 90
c = 152.489γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance