4F2N | pdb_00004f2n

Crystal structure of iron superoxide dismutase from Leishmania major

PDB DOI: https://doi.org/10.2210/pdb4F2N/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leishmania major
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-05-08 Released: 2012-05-16
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.203 (Depositor), 0.204 (DCC)
R-Value Work:
0.173 (Depositor), 0.175 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Iron superoxide dismutases in eukaryotic pathogens: new insights from Apicomplexa and Trypanosoma structures.

Phan, I.Q., Davies, D.R., Moretti, N.S., Shanmugam, D., Cestari, I., Anupama, A., Fairman, J.W., Edwards, T.E., Stuart, K., Schenkman, S., Myler, P.J.

(2015) Acta Crystallogr F Struct Biol Commun 71: 615-621

PubMed: 25961325 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X15004185
Primary Citation Related Structures:
4F2N, 4H3E, 4YET

PubMed Abstract:
Prior studies have highlighted the potential of superoxide dismutases as drug targets in eukaryotic pathogens. This report presents the structures of three iron-dependent superoxide dismutases (FeSODs) from Trypanosoma cruzi, Leishmania major and Babesia bovis. Comparison with existing structures from Plasmodium and other trypanosome isoforms shows a very conserved overall fold with subtle differences. In particular, structural data suggest that B. bovis FeSOD may display similar resistance to peroxynitrite-mediated inactivation via an intramolecular electron-transfer pathway as previously described in T. cruzi FeSOD isoform B, thus providing valuable information for structure-based drug design. Furthermore, lysine-acetylation results in T. cruzi indicate that acetylation occurs at a position close to that responsible for the regulation of acetylation-mediated activity in the human enzyme.

Organizational Affiliation

Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.

Macromolecule Content

Total Structure Weight: 313.94 kDa
Atom Count: 21,527
Modeled Residue Count: 2,513
Deposited Residue Count: 2,760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	230	Leishmania major	Mutation(s): 0 Gene Names: FESODA, LMJF_08_0290 EC: 1.15.1.1
UniProt
Find proteins for Q4QIE0 (Leishmania major) Explore Q4QIE0 Go to UniProtKB: Q4QIE0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4QIE0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain V [auth J] SDF format, chain W [auth K] SDF format, chain X [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth K] MOL2 format, chain X [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth I] mmCIF format, chain V [auth J] mmCIF format, chain W [auth K] mmCIF format, chain X [auth L]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.203 (Depositor), 0.204 (DCC)
R-Value Work: 0.173 (Depositor), 0.175 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.03	α = 91.66
b = 102.74	β = 96.36
c = 168.24	γ = 95.01

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
XDS	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-05-16

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2012-05-16
Type: Initial release
Version 1.1: 2015-06-03
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description