7XVX

Neutron crystal structure of human macrophage migration inhibitory factor

• PDB DOI: https://doi.org/10.2210/pdb7XVX/pdb

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


• Deposited: 2022-05-25 Released: 2023-05-31 
• Deposition Author(s): Ezawa, T., Tamada, T., Odaka, M., Matsumura, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.169 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.180 

Starting Model: experimental

Literature

Neutron crystal structure of human macrophage migration inhibitory factor

Ezawa, T., Nakagaki, T., Sugishima, K., Ishida, T., Hirano, Y., Kusaka, K., Tamada, T., Odaka, M., Wakui, H., Matsumura, H.

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: 37.07 kDa 
• Atom Count: 2,971 
• 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.169 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 3₁ 2 1

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.180 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.534	α = 90
b = 96.534	β = 90
c = 105.596	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Ezawa, T., Tamada, T., Odaka, M., Matsumura, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19K07011

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description