8ZLD

Crystal structure of PfHO from Plasmodium falciparum at 2.78 A

PDB DOI: https://doi.org/10.2210/pdb8ZLD/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Plasmodium falciparum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-05-18 Released: 2024-09-04
Deposition Author(s): Caaveiro, J.M.M., Senoo, A.
Funding Organization(s): Burroughs Wellcome Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.264
R-Value Work: 0.203
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

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

Literature

Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis

Blackwell, A.M., Jami-Alahmadi, Y., Nasamu, A.S., Kudo, S., Senoo, A., Slam, C., Tsumoto, K., Wohlschlegel, J.A., Caaveiro, J.M., Goldberg, D.E., Sigala, P.A.

(2024) Elife

DOI: https://doi.org/10.7554/elife.100256.1

Macromolecule Content

Total Structure Weight: 56.21 kDa
Atom Count: 3,108
Modelled Residue Count: 367
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase	A, B	232	Plasmodium falciparum	Mutation(s): 0 Gene Names: PF3D7_1011900
UniProt
Find proteins for Q8IJS6 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJS6 Go to UniProtKB: Q8IJS6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IJS6
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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.264
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.91	α = 90
b = 55.37	β = 90
c = 162.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Caaveiro, J.M.M.

Funding Organization	Location	Grant Number
Burroughs Wellcome Fund	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-09-04
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.