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 Macrophage migration inhibitory factor from Plasmodium vivax

Lovell, S., Liu, L., Cooper, A., Battaile, K.P.

To be published.

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