8TT9

X-ray structure of Macrophage Migration Inhibitory Factor (MIF) Covalently Bound to 4-hydroxyphenylpyruvate (HPP)

• PDB DOI: https://doi.org/10.2210/pdb8TT9/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-13 Released: 2024-08-28 
• Deposition Author(s): Schroder, G.C., Meilleur, F., Nix, J.C., Crichlow, G.V., Lolis, E.J.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.199 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

X-ray structure of Macrophage Migration Inhibitory Factor (MIF) Covalently Bound to 4-hydroxyphenylpyruvate (HPP)

Schroder, G.C., Crichlow, G.V., Zambrzycka, E., Pantouris, G., Nix, J.C., Chayen, N., Meilleur, F., Lolis, E.

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)

Macromolecule Content

• Total Structure Weight: 37.73 kDa 
• Atom Count: 3,003 
• Modelled Residue Count: 342 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C	114	Homo sapiens	Mutation(s): 0  Gene Names: MIF, GLIF, MMIF EC: 5.3.2.1 (PDB Primary Data), 5.3.3.12 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14174 (Homo sapiens) Explore P14174  Go to UniProtKB:  P14174
PHAROS:  P14174 GTEx:  ENSG00000240972

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ENO (Subject of Investigation/LOI)	D [auth A], G [auth B], H [auth C]	3-(4-HYDROXY-PHENYL)PYRUVIC ACID C9 H8 O4 KKADPXVIOXHVKN-UHFFFAOYSA-N
IPA	E [auth A], F [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.199 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.57	α = 90
b = 68.87	β = 90
c = 88.43	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Schroder, G.C., Meilleur, F., Nix, J.C., Crichlow, G.V., Lolis, E.J.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Structure summary