› 2vm9

X-ray diffraction
1.75Å resolution

Native structure of the recombinant discoidin II of Dictyostelium discoideum at 1.75 angstrom

Released:
DOI: 10.2210/pdb2vm9/pdb
PDB entry 2vm9 coloured by chain, front view.
PDB entry 2vm9 coloured by chain, side view.
PDB entry 2vm9 coloured by chain, top view.
Source organism: Dictyostelium discoideum AX2
Primary publication:
Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain.
Aragão KS, Satre M, Imberty A, Varrot A
Proteins 73 43-52 (2008)
PMID: 18384150

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154660 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Discoidin-2 Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 28.61 KDa
Source organism: Dictyostelium discoideum AX2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P42530 (Residues: 1-257; Coverage: 100%)
Gene names: DDB_G0292552, dscE
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand CA 1 x CA
Ligand MPD 2 x MPD
Ligand PO4 3 x PO4
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: R32
Unit cell:
a: 81.833Å b: 81.833Å c: 257.823Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.151 0.15 0.178
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Eat Prey, Live: Dictyostelium discoideum As a Model for Cell-Autonomous Defenses.
Dunn et al. (2017)
4 more

2 mentions without citation

Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers.
Buth et al. (2018)
1 more