4LSI: Ion selectivity of OmpF porin soaked in 0.3M KBr

Ion selectivity of OmpF porin soaked in 0.3M KBr. Determined by X-ray diffraction at 2.09 Å resolution. Released 23 Oct 2013.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Escherichia coli
Chains: 3
Atoms: 8,472
Mol. weight: 114.98 kDa
Ligands: C8E, MG
Released: 23 Oct 2013

Explore 4LSI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LSI contains 14 α-helices and 74 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	1
β-strand	14-23	10	1
β-strand	31	1	2
β-strand	36-37	2	1
β-strand	40-50	11	1
β-strand	55-66	12	1
β-strand	80-90	11	1
β-strand	94-102	9	1
α-helix	106-109	4
β-strand	132-141	10	1
α-helix	143-146	4
β-strand	151-158	8	1
α-helix	159-160	2
β-strand	161	1	3
β-strand	170	1	3
β-strand	173-182	10	1
β-strand	185-195	11	1
α-helix	196-197	2
α-helix	198-201	4
β-strand	205	1	4
β-strand	210-222	13	1
β-strand	225-235	11	1
β-strand	239-242	4	4
β-strand	247-250	4	4
β-strand	253-263	11	1
β-strand	269-283	15	1
β-strand	287-302	16	1
β-strand	307-316	10	1
β-strand	329	1	2
β-strand	331-339	9	1

Chain B: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	9-23	15	5
β-strand	31	1	6
β-strand	36-37	2	5
β-strand	40-52	13	5
β-strand	55-66	12	5
β-strand	80-90	11	5
β-strand	94-100	7	5
β-strand	102	1	7
α-helix	106-109	4
β-strand	132	1	7
β-strand	136-141	6	5
α-helix	143-146	4
β-strand	151-158	8	5
β-strand	161	1	8
β-strand	170	1	8
β-strand	173-182	10	5
β-strand	185-195	11	5
α-helix	196-197	2
α-helix	198-201	4
β-strand	205	1	9
β-strand	210-222	13	5
β-strand	225-235	11	5
β-strand	239-242	4	9
β-strand	247-250	4	9
β-strand	253-263	11	5
β-strand	269-283	15	5
β-strand	287-302	16	5
β-strand	307-316	10	5
β-strand	329	1	6
β-strand	331-339	9	5

Chain C: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	10
β-strand	14-23	10	10
β-strand	31	1	11
β-strand	36-37	2	10
β-strand	40-50	11	10
β-strand	55-66	12	10
β-strand	80-90	11	10
β-strand	94-102	9	10
α-helix	106-109	4
β-strand	132-141	10	10
α-helix	143-146	4
β-strand	151-158	8	10
α-helix	159-160	2
β-strand	161	1	12
β-strand	170	1	12
β-strand	173-182	10	10
β-strand	185-195	11	10
α-helix	196-197	2
α-helix	198-201	4
β-strand	205	1	10
β-strand	210-222	13	10
β-strand	225-241	17	10
β-strand	248-263	16	10
β-strand	269-283	15	10
β-strand	287-304	18	10
β-strand	307-316	10	10
β-strand	329	1	11
β-strand	331-339	9	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein F	A, B, C	protein	341	Escherichia coli	P02931 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>4LSI_1 Outer membrane protein F (chains A, B, C)
GAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYG
QWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFG
GDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSIS
YEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATP
ITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGA
TYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF

Ligands and cofactors

ID	Name	Formula	Copies
C8E	(hydroxyethyloxy)tri(ethyloxy)octane	C16 H34 O5	4
MG	Magnesium ion	Mg	8

Water and common crystallization additives (PEG, GOL, BR) are not listed.

Primary citation

A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. Dhakshnamoorthy, B., Ziervogel, B.K., Blachowicz, L. et al. J Am Chem Soc (2013) 135:16561-16568. DOI 10.1021/ja407783a · PubMed

Other PDB entries of the same protein (UniProt P02931 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZFG 1.59 Å, Structure of OMPF PORIN
4GCS 1.87 Å, Crystal Structure of E. coli OmpF porin in complex with Ertapenem
3POQ 1.9 Å, Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, small…
4LSF 1.9 Å, Ion selectivity of OmpF soaked in 0.1M KBr
6ZHV 1.95 Å, Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
4GCP 1.98 Å, Crystal Structure of E. coli OmpF porin in complex with Ampicillin
3POX 2.0 Å, Crystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1
6ZHP 2.05 Å, Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
4LSE 2.1 Å, Ion selectivity of OmpF porin soaked in 0.2M NaBr
1HXX 2.2 Å, Ompf porin mutant Y106F
4GCQ 2.2 Å, Crystal Structure of E. coli OmpF porin in complex with Carbenicillin
4LSH 2.2 Å, Ion selectivity of OmpF porin soaked in 0.2M KBr

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