› 5ak8

X-ray diffraction
1.48Å resolution

Structure of C351A mutant of Porphyromonas gingivalis peptidylarginine deiminase

Released:
DOI: 10.2210/pdb5ak8/pdb
PDB entry 5ak8 coloured by chain, front view.
PDB entry 5ak8 coloured by chain, side view.
PDB entry 5ak8 coloured by chain, top view.
Source organism: Porphyromonas gingivalis
Primary publication:
Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase: implications for autoimmunity in rheumatoid arthritis.
Montgomery AB, Kopec J, Shrestha L, Thezenas ML, Burgess-Brown NA, Fischer R, Yue WW, Venables PJ
Ann Rheum Dis 75 1255-61 (2016)
PMID: 26209657

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193236 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidylarginine deiminase Chain: A
Molecule details ›
Chain: A
Length: 438 amino acids
Theoretical weight: 48.91 KDa
Source organism: Porphyromonas gingivalis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9RQJ2 (Residues: 49-484; Coverage: 82%)
Gene name: PG_1424
Sequence domains: Porphyromonas-type peptidyl-arginine deiminase
Structure domains: L-arginine/glycine Amidinotransferase; Chain A

Ligands and Environments

4 bound ligands:
Ligand ALA 1 x ALA
Ligand ARG 1 x ARG
Ligand NA 1 x NA
Ligand EDO 18 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 101.79Å b: 84.09Å c: 55.46Å
α: 90° β: 92.64° γ: 90°
R-values:
R R work R free
0.129 0.127 0.164
Expression system: Escherichia coli BL21(DE3)

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Citations

23 review citations

Neutrophil Extracellular Traps in Autoimmunity and Allergy: Immune Complexes at Work.
Granger et al. (2019)
22 more