› 3d0f

X-ray diffraction
1.64Å resolution

Structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718

Released:
DOI: 10.2210/pdb3d0f/pdb
PDB entry 3d0f coloured by chain, front view.
PDB entry 3d0f coloured by chain, side view.
PDB entry 3d0f coloured by chain, top view.
Source organism: Nitrosomonas europaea ATCC 19718
Entry authors: Cuff ME, Mulligan R, Clancy S, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Reactions 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
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182625 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Penicillin-binding protein 1A Chains: A, B
Molecule details ›
Chains: A, B
Length: 106 amino acids
Theoretical weight: 11.7 KDa
Source organism: Nitrosomonas europaea ATCC 19718
Expression system: Escherichia coli
UniProt:
  • Canonical: Q81ZZ3 (Residues: 318-420; Coverage: 13%)
Gene names: NE2317, mrcA
Sequence domains: Penicillin-binding protein OB-like domain
Structure domains: Nucleic acid-binding proteins

Ligands and Environments

2 bound ligands:
Ligand PO4 1 x PO4
Ligand GOL 1 x GOL
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 38.206Å b: 52.219Å c: 56.86Å
α: 90° β: 107.87° γ: 90°
R-values:
R R work R free
0.173 0.17 0.217
Expression system: Escherichia coli

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