› 1n13

X-ray diffraction
1.4Å resolution

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

Released:
DOI: 10.2210/pdb1n13/pdb
PDB entry 1n13 coloured by chain, front view.
PDB entry 1n13 coloured by chain, side view.
PDB entry 1n13 coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms.
Tolbert WD, Graham DE, White RH, Ealick SE
Structure 11 285-94 (2003)
PMID: 12623016

Function and Biology Details

Reaction catalysed: 
L-arginine = agmatine + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176469 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Pyruvoyl-dependent arginine decarboxylase subunit beta Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
Length: 52 amino acids
Theoretical weight: 5.43 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57764 (Residues: 1-52; Coverage: 32%)
Gene names: MJ0316, pdaD
Structure domains: Wheat Germ Agglutinin (Isolectin 2); domain 1
Pyruvoyl-dependent arginine decarboxylase subunit alpha Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
Length: 113 amino acids
Theoretical weight: 12.3 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57764 (Residues: 54-165; Coverage: 68%)
Gene names: MJ0316, pdaD
Sequence domains: Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
Structure domains: Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

Ligands and Environments

2 bound ligands:
Ligand AG2 6 x AG2
Ligand MRD 8 x MRD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F2, APS BEAMLINE 8-BM
Spacegroup: P21
Unit cell:
a: 56.46Å b: 92.88Å c: 87.11Å
α: 90° β: 94.74° γ: 90°
R-values:
R R work R free
0.196 0.192 0.215
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Polyamines in Eukaryotes, Bacteria, and Archaea.
Michael AJ. (2016)
1 more

3 mentions without citation

Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.
Chen et al. (2012)
2 more