› 5bmq

X-ray diffraction
2.05Å resolution

Crystal structure of L,D-transpeptidase (Yku) from Stackebrandtia nassauensis

Released:
DOI: 10.2210/pdb5bmq/pdb
PDB entry 5bmq coloured by chain, front view.
PDB entry 5bmq coloured by chain, side view.
PDB entry 5bmq coloured by chain, top view.
Source organism: Stackebrandtia nassauensis DSM 44728
Entry authors: Chang C, Bigelow L, Clancy S, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112535 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L,D-TPase catalytic domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 243 amino acids
Theoretical weight: 27.03 KDa
Source organism: Stackebrandtia nassauensis DSM 44728
Expression system: Escherichia coli
UniProt:
  • Canonical: D3Q1D9 (Residues: 61-303; Coverage: 80%)
Gene name: Snas_6095
Sequence domains: L,D-transpeptidase catalytic domain

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand DIO 1 x DIO
Ligand GOL 1 x GOL
1 modified residue:
Ligand MSE 3 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I213
Unit cell:
a: 143.356Å b: 143.356Å c: 143.356Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.154 0.178
Expression system: Escherichia coli

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