› 4riz

X-ray diffraction
2.2Å resolution

The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745

Released:
DOI: 10.2210/pdb4riz/pdb
PDB entry 4riz coloured by chain, front view.
PDB entry 4riz coloured by chain, side view.
PDB entry 4riz coloured by chain, top view.
Source organism: Sphaerobacter thermophilus DSM 20745
Entry authors: Wu R, Clancy S, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Reaction catalysed: 
L-glutamate = 4-aminobutanoate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112284 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal-dependent decarboxylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 486 amino acids
Theoretical weight: 53.08 KDa
Source organism: Sphaerobacter thermophilus DSM 20745
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D1C7D8 (Residues: 1-483; Coverage: 100%)
Gene name: Sthe_2364
Sequence domains: Pyridoxal-dependent decarboxylase conserved domain
Structure domains:

Ligands and Environments


Cofactor: Ligand PMP 3 x PMP
2 bound ligands:
Ligand NA 3 x NA
Ligand GOL 4 x GOL
1 modified residue:
Ligand LLP 4 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 69.411Å b: 124.659Å c: 131.849Å
α: 90° β: 99.42° γ: 90°
R-values:
R R work R free
0.16 0.157 0.199
Expression system: Escherichia coli BL21(DE3)

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