› 1t35

X-ray diffraction
2.72Å resolution

CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YVDD- A PUTATIVE LYSINE DECARBOXYLASE

Released:
DOI: 10.2210/pdb1t35/pdb
PDB entry 1t35 coloured by chain, front view.
PDB entry 1t35 coloured by chain, side view.
PDB entry 1t35 coloured by chain, top view.
Source organism: Bacillus subtilis
Entry authors: Rajashankar KR, Kniewel R, Solorzano V, Lima CD, Burley SK, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
L-lysine = cadaverine + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126553 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
LOG family protein YvdD Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 191 amino acids
Theoretical weight: 21.64 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: O06986 (Residues: 1-191; Coverage: 100%)
Gene names: BSU34640, yvdD
Sequence domains: Possible lysine decarboxylase
Structure domains: Rossmann fold

Ligands and Environments

1 bound ligand:
Ligand SO4 14 x SO4
1 modified residue:
Ligand MSE 96 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21212
Unit cell:
a: 117.562Å b: 170.773Å c: 89.721Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.251 0.243 0.286
Expression system: Escherichia coli

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