› 4r0q

X-ray diffraction
2Å resolution

Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with cephalothin

Released:
DOI: 10.2210/pdb4r0q/pdb
PDB entry 4r0q coloured by chain, front view.
PDB entry 4r0q coloured by chain, side view.
PDB entry 4r0q coloured by chain, top view.
Source organism: Lancefieldella parvulum DSM 20469
Entry authors: Filippova EV, Minasov G, Kiryukhina O, Clancy S, Joachimiak A, Anderson WF, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Reaction catalysed: 
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111806 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Penicillin-binding protein transpeptidase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 482 amino acids
Theoretical weight: 50.65 KDa
Source organism: Lancefieldella parvulum DSM 20469
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C8W8H7 (Residues: 505-954; Coverage: 47%)
Gene name: Apar_1344
Sequence domains: Penicillin binding protein transpeptidase domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand CEP 2 x CEP
Ligand SCN 2 x SCN
Ligand B3P 2 x B3P
1 modified residue:
Ligand MSE 28 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21
Unit cell:
a: 68.553Å b: 70.002Å c: 115.233Å
α: 90° β: 96.76° γ: 90°
R-values:
R R work R free
0.181 0.179 0.217
Expression system: Escherichia coli BL21(DE3)

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