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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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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:

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.