3ONR

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

• PDB DOI: https://doi.org/10.2210/pdb3ONR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-08-30 Released: 2011-03-16 
• Deposition Author(s): Arulandu, A., Sacchettini, J.C.

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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 

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

• PubMed: 21370306 
• DOI: https://doi.org/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. Structure and sequence analysis were used to identify orthologs of Rv0379 with different ligand-binding specificity.

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Organizational Affiliation: 

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

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: 97.88 kDa 
• Atom Count: 6,869 
• Modelled Residue Count: 838 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN TRANSPORT PROTEIN SECE2	A, B, C, D, E, F, G, H, I, J, K, L	72	Mycobacterium tuberculosis	Mutation(s): 2  Gene Names: Rv0379, secE2
UniProt
Find proteins for Q6MX43 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore Q6MX43  Go to UniProtKB:  Q6MX43

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	AA [auth I], T [auth E], V [auth F]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
FMT	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
CA	BA [auth J], M [auth A], Q [auth D], W [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 70.193	α = 90
b = 78.446	β = 90
c = 152.489	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Arulandu, A., Sacchettini, J.C.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations