› 4rm1

X-ray diffraction
1.99Å resolution

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

Released:
DOI: 10.2210/pdb4rm1/pdb
PDB entry 4rm1 coloured by chain, front view.
PDB entry 4rm1 coloured by chain, side view.
PDB entry 4rm1 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 2 x PMP
2 bound ligands:
Ligand GOL 6 x GOL
Ligand CL 2 x CL
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: 69.548Å b: 125.004Å c: 132.242Å
α: 90° β: 99.62° γ: 90°
R-values:
R R work R free
0.17 0.169 0.203
Expression system: Escherichia coli BL21(DE3)

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