8AP3 | pdb_00008ap3

Structure of A. thaliana MIF/D-DT-like protein-2 (MDL2)

• PDB DOI: https://doi.org/10.2210/pdb8AP3/pdb

• Classification: CYTOKINE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-09 Released: 2023-08-23 
• Deposition Author(s): Manjula, R., Basquin, J., Lolis, E.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Structure of A. thaliana MIF/D-DT-like protein-2 (MDL2)

Manjula, R., Basquin, J., 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.18 kDa 
• Atom Count: 2,823 
• Modeled Residue Count: 351 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MIF homologue	A, B, C	122	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9M011 (Arabidopsis thaliana) Explore Q9M011  Go to UniProtKB:  Q9M011

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.218	α = 90
b = 79.243	β = 90
c = 84.6	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Manjula, R., Basquin, J., Lolis, E.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release