› 3td5

X-ray diffraction
2Å resolution

Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala

Released:
DOI: 10.2210/pdb3td5/pdb
PDB entry 3td5 coloured by chain, front view.
PDB entry 3td5 coloured by chain, side view.
PDB entry 3td5 coloured by chain, top view.
Source organism: Acinetobacter baumannii
Primary publication:
Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane.
Park JS, Lee WC, Yeo KJ, Ryu KS, Kumarasiri M, Hesek D, Lee M, Mobashery S, Song JH, Kim SI, Lee JC, Cheong C, Jeon YH, Kim HY
FASEB J 26 219-28 (2012)
PMID: 21965596

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164071 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Outer membrane protein Omp38 Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 123 amino acids
Theoretical weight: 13.88 KDa
Source organism: Acinetobacter baumannii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6RYW5 (Residues: 221-339; Coverage: 35%)
Gene names: HMPREF0010_02782, omp38, ompA
Sequence domains: OmpA family
Structure domains: OmpA-like domain
peptide(L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala) Chains: I, J, K, L, M, N, O, P
Molecule details ›
Chains: I, J, K, L, M, N, O, P
Length: 5 amino acids
Theoretical weight: 533 Da
Source organism: Acinetobacter baumannii
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CL 6 x CL
3 modified residues:
Ligand FGA 8 x FGA
Ligand API 8 x API
Ligand DAL 16 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21
Unit cell:
a: 65.09Å b: 162.61Å c: 66.228Å
α: 90° β: 112.68° γ: 90°
R-values:
R R work R free
0.22 0.22 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

20 review citations

Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions.
Schwechheimer et al. (2015)
19 more

7 mentions without citation

Interaction with the host: the role of fibronectin and extracellular matrix proteins in the adhesion of Gram-negative bacteria.
Vaca et al. (2020)
6 more