4D5U image
Deposition Date 2014-11-07
Release Date 2015-12-16
Last Version Date 2023-12-20
Entry Detail
PDB ID:
4D5U
Title:
Structure of OmpF in I2
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.50 Å
R-Value Free:
0.28
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
I 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:OUTER MEMBRANE PROTEIN F
Gene (Uniprot):ompF
Chain IDs:A, B, C, D, E, F
Chain Length:340
Number of Molecules:6
Biological Source:ESCHERICHIA COLI
Ligand Molecules
Primary Citation
Two Different Centered Monoclinic Crystals of the E. Coli Outer-Membrane Protein Ompf Originate from the Same Building Block.
Biochim.Biophys.Acta 1858 326 ? (2016)
PMID: 26620074 DOI: 10.1016/J.BBAMEM.2015.11.021

Abstact

Macromolecule crystal formation can be divided in two major steps: 1. the formation of a nucleus and 2. the growth of this nucleus into a full mature crystal. The latter is well described and understood, while the former remains elusive due to the difficulty to study it and is described by nucleation theories. Here we report the structure of the Escherichia coli outer membrane porin OmpF in two centered monoclinic space groups. Strikingly, the two crystals originate from the same building block, made of two trimers of OmpF interacting via their rough side. The different crystallization conditions trigger the formation of distinct arrangement of these building blocks, leading to the formation of translational non-crystallographic symmetry (tNCS) in one case, made possible by the loose lateral packing mediated by detergents. In light of nucleation theories, these results allow us to speculate that these two crystals originate from nuclei made of either clusters of building blocks, or already forming columns that later associate laterally using detergents as glue.

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