3POX: OmpF protein

Crystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1. Determined by X-ray diffraction at 2.0 Å resolution. Released 7 Mar 2012.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Escherichia Coli
Chains: 6
Atoms: 18,507
Mol. weight: 255.19 kDa
Ligands: OLC, SCN
Released: 7 Mar 2012

Explore 3POX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3POX contains 25 α-helices and 140 β-strands across 6 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	2-6	5	1
β-strand	9-23	15	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	144-146	3
β-strand	151-158	8	1
β-strand	161	1	3
α-helix	166-168	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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
β-strand	9-23	15	5
β-strand	31	1	6
β-strand	36-37	2	5
β-strand	40-50	11	5
β-strand	55-66	12	5
β-strand	80-90	11	5
β-strand	94-102	9	5
α-helix	106-109	4
β-strand	132-142	11	5
α-helix	144-146	3
β-strand	151-158	8	5
β-strand	161	1	7
β-strand	170	1	7
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	5
β-strand	210-222	13	5
β-strand	225-242	18	5
β-strand	247-263	17	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	2-6	5	8
β-strand	9-23	15	8
β-strand	31	1	9
β-strand	36-37	2	8
β-strand	40-50	11	8
β-strand	55-66	12	8
β-strand	80-90	11	8
β-strand	94-102	9	8
α-helix	106-109	4
β-strand	132-141	10	8
α-helix	143-146	4
β-strand	151-158	8	8
β-strand	161	1	10
α-helix	166-168	3
β-strand	170	1	10
β-strand	173-182	10	8
β-strand	185-195	11	8
α-helix	196-197	2
α-helix	198-201	4
β-strand	205	1	8
β-strand	210-222	13	8
β-strand	225-241	17	8
β-strand	248-263	16	8
β-strand	269-283	15	8
β-strand	287-302	16	8
β-strand	307-316	10	8
β-strand	329	1	9
β-strand	331-339	9	8

Chain D: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
β-strand	9-23	15	11
β-strand	31	1	12
β-strand	36-37	2	11
β-strand	40-50	11	11
β-strand	55-66	12	11
β-strand	80-90	11	11
β-strand	94-102	9	11
α-helix	106-109	4
β-strand	132-141	10	11
β-strand	151-158	8	11
α-helix	159-160	2
β-strand	161	1	13
α-helix	166-168	3
β-strand	170	1	13
β-strand	173-182	10	11
β-strand	185-195	11	11
α-helix	196-197	2
α-helix	198-201	4
β-strand	205	1	11
β-strand	210-222	13	11
β-strand	225-241	17	11
β-strand	248-263	16	11
β-strand	269-283	15	11
β-strand	287-302	16	11
β-strand	307-316	10	11
β-strand	329	1	12
β-strand	331-339	9	11

Chain E: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	14
β-strand	9-23	15	14
β-strand	31	1	15
β-strand	36-37	2	14
β-strand	40-50	11	14
β-strand	55-66	12	14
β-strand	80-90	11	14
β-strand	94-102	9	14
α-helix	106-109	4
β-strand	132-142	11	14
α-helix	144-146	3
β-strand	151-158	8	14
β-strand	161	1	16
β-strand	170	1	16
β-strand	173-182	10	14
β-strand	185-195	11	14
α-helix	196-197	2
α-helix	198-202	5
β-strand	205	1	14
β-strand	210-222	13	14
β-strand	225-242	18	14
β-strand	247-263	17	14
β-strand	269-283	15	14
β-strand	287-302	16	14
β-strand	307-316	10	14
β-strand	329	1	15
β-strand	331-339	9	14

Chain F: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	17
β-strand	9-23	15	17
β-strand	31	1	18
β-strand	36-37	2	17
β-strand	40-50	11	17
β-strand	55-66	12	17
β-strand	80-90	11	17
β-strand	94-102	9	17
α-helix	106-109	4
β-strand	132-141	10	17
β-strand	151-158	8	17
β-strand	161	1	19
β-strand	170	1	19
β-strand	173-182	10	17
β-strand	185-195	11	17
α-helix	198-201	4
β-strand	205	1	17
β-strand	210-222	13	17
β-strand	225-242	18	17
β-strand	247-263	17	17
β-strand	269-283	15	17
β-strand	287-302	16	17
β-strand	307-316	10	17
β-strand	329	1	18
β-strand	331-339	9	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
OmpF protein	A, B, C, D, E, F	protein	340	Escherichia Coli	P02931 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>3POX_1 OmpF protein (chains A, B, C, D, E, F)
AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQ
WEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGG
DTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISY
EYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPI
TNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGAT
YYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	88
SCN	Thiocyanate ion	C N S	6

Water and common crystallization additives (K) are not listed.

Primary citation

Structure of Escherichia coli OmpF porin from lipidic mesophase. Efremov, R.G., Sazanov, L.A. J Struct Biol (2012) 178:311-318. DOI 10.1016/j.jsb.2012.03.005 · 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
6ZHP 2.05 Å, Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
4LSI 2.09 Å, Ion selectivity of OmpF porin soaked in 0.3M KBr
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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