9K2L | pdb_00009k2l

Crystal structure of Plasmoredoxin, a disulfide oxidoreductase from Plasmodium falciparum crystallized in the presence of Glutathione(GSH)

PDB DOI: https://doi.org/10.2210/pdb9K2L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-10-17 Released: 2024-10-30
Deposition Author(s): Panicker, L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.210 (Depositor), 0.206 (DCC)
R-Value Work:
0.173 (Depositor), 0.177 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Plasmoredoxin, a disulfide oxidoreductase from Plasmodium falciparum crystallized in the presence of Glutathione(GSH)

Panicker, L.

To be published.

Macromolecule Content

Total Structure Weight: 26.08 kDa
Atom Count: 1,571
Modeled Residue Count: 168
Deposited Residue Count: 212
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmoredoxin	A	212	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF3D7_0303600
UniProt
Find proteins for Q8I224 (Plasmodium falciparum (isolate 3D7)) Explore Q8I224 Go to UniProtKB: Q8I224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8I224
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.210 (Depositor), 0.206 (DCC)
R-Value Work: 0.173 (Depositor), 0.177 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data: https://doi.org/10.5281/zenodo.13953867

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.162	α = 90
b = 50.348	β = 90
c = 77.888	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	India	NA

Revision History (Full details and data files)

Version 1.0: 2024-10-30
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.