› 5nur

X-ray diffraction
3.29Å resolution

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

Released:
DOI: 10.2210/pdb5nur/pdb
PDB entry 5nur coloured by chain, front view.
PDB entry 5nur coloured by chain, side view.
PDB entry 5nur coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for maintenance of bacterial outer membrane lipid asymmetry.
Abellón-Ruiz J, Kaptan SS, Baslé A, Claudi B, Bumann D, Kleinekathöfer U, van den Berg B
Nat Microbiol 2 1616-1623 (2017)
PMID: 29038444

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-494906 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (5 distinct):
Outer membrane porin F Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 340 amino acids
Theoretical weight: 37.11 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P02931 (Residues: 23-362; Coverage: 100%)
Gene names: JW0912, b0929, cmlB, coa, cry, ompF, tolF
Sequence domains: Gram-negative porin
Structure domains: Porin
ABC transporter permease Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 236 amino acids
Theoretical weight: 26.36 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0W8AQT6 (Residues: 18-253; Coverage: 93%)
Gene names: APT92_13155, B6I68_03735, BANRA_01481, BANRA_03289, BL124_00010915, BV369_04705, CP554_06070, DM083_10750, DW281_04185, EAO17_05790, EXT45_18435, FME62_07510, FXN67_06360, G4V31_07835, GJJ01_13475, GJJ08_007755, GJJ18_12455, GNF00_22240, H3G96_019975, HV185_19080, I8R04_05255, JMZ77_07170, KPZU09_72170, LS45_12510, NCTC11679_01560, NCTC13443_05414, NCTC13465_02422, NCTC204_04024, NCTC5047_06653, NCTC5052_03096, NCTC5053_06125, NCTC8849_04376, NCTC9140_05972, NCTC9601_01045, NCTC9617_05977, NCTC9637_02226, NCTC9645_04093, NCTC9661_02390, Q6294_07245, SAMEA2273558_01513, SAMEA3499874_02731, SAMEA3499901_01895, SAMEA3515122_01898, SAMEA3538551_02161, SAMEA3538828_02283, SAMEA3649591_00923, SAMEA3649615_01943, SAMEA3720909_00232, SAMEA3729652_02006, SAMEA4364603_01402, SAMEA4873597_02024, SAMEA4873632_02225, mlaA
Sequence domains: MlaA lipoprotein

Ligands and Environments

Carbohydrate polymer : NEW Components: GP1, Z9M, KDO
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GP1, Z9M, KDO
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GP1, Z9M, KDO
Carbohydrate polymer
3 bound ligands:
Ligand CA 3 x CA
Ligand SO4 8 x SO4
Ligand C8E 3 x C8E
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 190.55Å b: 179.66Å c: 133.39Å
α: 90° β: 116.55° γ: 90°
R-values:
R R work R free
0.221 0.219 0.259
Expression system: Escherichia coli

Quick links

Citations

17 review citations

Computational Modeling of Realistic Cell Membranes.
Marrink et al. (2019)
16 more

1 mention without citation

Therapeutics for COVID-19: from computation to practices-where we are, where we are heading to.
Ojha et al. (2021)