3ONR | pdb_00003onr

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.229 (Depositor), 0.248 (DCC)
R-Value Work:
0.181 (Depositor), 0.203 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 21370306 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.607

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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 97.88 kDa
Atom Count: 6,869
Modeled Residue Count: 838
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN TRANSPORT PROTEIN SECE2	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6MX43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain AA [auth I] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain AA [auth I] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain AA [auth I]	AA [auth I], T [auth E], V [auth F]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain AA [auth I] Focus chain T [auth E] Focus chain V [auth F]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain Y [auth H] SDF format, chain X [auth G] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain EA [auth L] SDF format, chain DA [auth K] SDF format, chain CA [auth J] MOL2 format, chain Z [auth I] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth G] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain EA [auth L] MOL2 format, chain DA [auth K] MOL2 format, chain CA [auth J] mmCIF format, chain Z [auth I] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth G] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain EA [auth L] mmCIF format, chain DA [auth K] mmCIF format, chain CA [auth J]	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		Interactions Focus chain CA [auth J] Focus chain DA [auth K] Focus chain EA [auth L] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth I] Interactions & Density Focus chain CA [auth J] Focus chain DA [auth K] Focus chain EA [auth L] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth I]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain W [auth G] SDF format, chain Q [auth D] SDF format, chain M [auth A] SDF format, chain BA [auth J] MOL2 format, chain W [auth G] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth A] MOL2 format, chain BA [auth J] mmCIF format, chain W [auth G] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth A] mmCIF format, chain BA [auth J]	BA [auth J], M [auth A], Q [auth D], W [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth J] Focus chain M [auth A] Focus chain Q [auth D] Focus chain W [auth G] Interactions & Density Focus chain BA [auth J] Focus chain M [auth A] Focus chain Q [auth D] Focus chain W [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.229 (Depositor), 0.248 (DCC)
R-Value Work: 0.181 (Depositor), 0.203 (DCC)
R-Value Observed: 0.183 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-03-16

Deposition Author(s):

Arulandu, A.

Sacchettini, J.C.

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
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations