› 2q4d

X-ray diffraction
2.15Å resolution

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950

Released:
DOI: 10.2210/pdb2q4d/pdb
PDB entry 2q4d coloured by chain, ensemble of 16 models, front view.
PDB entry 2q4d coloured by chain, ensemble of 16 models, side view.
PDB entry 2q4d coloured by chain, ensemble of 16 models, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Ensemble refinement of protein crystal structures: validation and application.
Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN
Structure 15 1040-52 (2007)
PMID: 17850744

Function and Biology Details

Reaction catalysed: 
N(6)-(Delta(2)-isopentenyl)-adenosine 5'-phosphate + H(2)O = N(6)-(dimethylallyl)adenine + D-ribose 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183058 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG8 Chains: A, B
Molecule details ›
Chains: A, B
Length: 216 amino acids
Theoretical weight: 24.24 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q84MC2 (Residues: 2-216; Coverage: 100%)
Gene names: At5g11950, F14F18.120, LOG8
Sequence domains: Possible lysine decarboxylase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand NO3 1 x NO3
Ligand EDO 4 x EDO
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
Spacegroup: C2
Unit cell:
a: 121.589Å b: 80.427Å c: 50.709Å
α: 90° β: 102.97° γ: 90°
R-values:
R R work R free
0.152 0.152 0.207
Expression system: Escherichia coli

Quick links

Citations

19 review citations

Enzymes in jasmonate biosynthesis - structure, function, regulation.
Schaller et al. (2009)
18 more

3 mentions without citation

Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling.
Burroughs et al. (2015)
2 more