9B0M | pdb_00009b0m

Crystal structure of Macrophage migration inhibitory factor from Plasmodium vivax

• PDB DOI: https://doi.org/10.2210/pdb9B0M/pdb

• Classification: CYTOKINE
• Organism(s): Plasmodium vivax Sal-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-12 Released: 2024-03-20 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Plasmodium vivax macrophage migration inhibitory factor

Nair, A., Lin, M., Srivastava, A., Liu, L., Cooper, A., Battaile, K.P., Harmon, E., Myler, P.J., Staker, B.L., Lovell, S., Chakafana, G., Asojo, O.A.

(2026) Acta Crystallogr F Struct Biol Commun 

• DOI: https://doi.org/10.1107/S2053230X26003870

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.12 kDa 
• Atom Count: 774 
• Modeled Residue Count: 96 
• Deposited Residue Count: 137 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-dopachrome isomerase	A	137	Plasmodium vivax Sal-1	Mutation(s): 0  Gene Names: PVX_124095 EC: 5.3.2.1 (PDB Primary Data), 5.3.3.12 (PDB Primary Data)
UniProt
Find proteins for A5K093 (Plasmodium vivax (strain Salvador I)) Explore A5K093  Go to UniProtKB:  A5K093

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.218 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m39b0m

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.457	α = 90
b = 75.457	β = 90
c = 36.947	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release
  
• Version 1.1: 2026-05-20
  Changes: Database references, Structure summary