8DQ6

Structure of A. thaliana MIF/D-DT-like protein-1 (MDL1)

• PDB DOI: https://doi.org/10.2210/pdb8DQ6/pdb

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


• Deposited: 2022-07-18 Released: 2023-07-26 
• Deposition Author(s): Manjula, R., Basquin, J., Lolis, E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.207 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

Structure of A. thaliana MIF/D-DT-like protein-1 (AtMDL1)

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: 35.33 kDa 
• Atom Count: 2,437 
• Modelled Residue Count: 309 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MIF/D-DT-like protein-1	A, B, C	109	Arabidopsis thaliana	Mutation(s): 0  Gene Names: MUL3.12, MUL3_12, At5g57170, At5g57170/MUL3_12
UniProt
Find proteins for Q9LU69 (Arabidopsis thaliana) Explore Q9LU69  Go to UniProtKB:  Q9LU69

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.207 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.737	α = 90
b = 66.737	β = 90
c = 132.32	γ = 120

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: 2023-07-26 
Deposition Author(s): Manjula, R., Basquin, J., Lolis, E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection