1FIM

MACROPHAGE MIGRATION INHIBITORY FACTOR

• PDB DOI: https://doi.org/10.2210/pdb1FIM/pdb

• Classification: CYTOKINE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-01-31 Released: 1996-07-11 
• Deposition Author(s): Suzuki, M., Sugimoto, H., Nakagawa, A., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Crystal structure of the macrophage migration inhibitory factor from rat liver.

Suzuki, M., Sugimoto, H., Nakagawa, A., Tanaka, I., Nishihira, J., Sakai, M.

(1996) Nat Struct Biol 3: 259-266

• PubMed: 8605628 
• DOI: https://doi.org/10.1038/nsb0396-259
• Primary Citation of Related Structures:  
  1FIM


• PubMed Abstract: 
  

  The tertiary structure of the macrophage migration inhibitory factor (MIF) from rat liver (12,300 Mr) is presented at 2.2 A resolution. Each monomer consists of two beta/alpha/beta motifs aligned in quasi two-fold symmetry, comprising a domain consisting of a four-stranded mixed beta-sheet and two antiparallel alpha-helices. The protein exists as a trimer in the crystal. An extra beta-strand that is almost perpendicular to the other beta-strands joins to the beta-sheet of the neighbouring monomer in the trimer. Unexpected similarities were detected between MIF and two kinds of isomerase.

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Organizational Affiliation: 

Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.28 kDa 
• Atom Count: 781 
• Modelled Residue Count: 103 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MACROPHAGE MIGRATION INHIBITORY FACTOR	A	114	Rattus norvegicus	Mutation(s): 3  EC: 5.3.3.12 (UniProt), 5.3.2.1 (UniProt)
UniProt
Find proteins for P30904 (Rattus norvegicus) Explore P30904  Go to UniProtKB:  P30904

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.8	α = 90
b = 61.8	β = 90
c = 53.4	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-07-11 
Deposition Author(s): Suzuki, M., Sugimoto, H., Nakagawa, A., Tanaka, I.

Revision History  

• Version 1.0: 1996-07-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.5: 2022-12-21
  Changes: Database references
• Version 1.6: 2024-11-13
  Changes: Data collection, Structure summary