2GYK: Colicin-E9 immunity protein

Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A). Determined by X-ray diffraction at 1.6 Å resolution. Released 15 May 2007.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Escherichia coli K12
Chains: 4
Atoms: 4,109
Mol. weight: 49.66 kDa
Ligands: PO4, ZN
Released: 15 May 2007

Explore 2GYK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2GYK contains 37 α-helices and 30 β-strands across 4 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.

Chains A and E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	11	1	1
α-helix	12-23	12
α-helix	30-44	15
α-helix	51-54	4
α-helix	56-57	2
α-helix	64-77	14
β-strand	84	1	1

Chain B: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	2
β-strand	12	1	3
β-strand	16	1	4
α-helix	22-27	6
β-strand	32-33	2	5
α-helix	34	1
β-strand	35	1	4
α-helix	36-42	7
β-strand	46-47	2	2
α-helix	50-63	14
α-helix	68-70	3
α-helix	73-80	8
α-helix	83-85	3
β-strand	86	1	6
α-helix	87-88	2
α-helix	89-91	3
β-strand	93	1	7
β-strand	96	1	7
β-strand	98	1	6
β-strand	100-103	4	5
α-helix	107-109	3
β-strand	115	1	3
α-helix	116-118	3
β-strand	119-122	4	5
α-helix	124-131	8

Chain F: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	9-10	2	9
β-strand	12	1	10
β-strand	16	1	11
α-helix	22-25	4
β-strand	32-33	2	12
α-helix	34	1
β-strand	35	1	11
α-helix	36-42	7
β-strand	46-47	2	9
α-helix	50-63	14
α-helix	65-68	4
α-helix	73-80	8
α-helix	83-85	3
β-strand	86	1	13
α-helix	87-88	2
α-helix	89-91	3
β-strand	93	1	14
β-strand	96	1	14
β-strand	98	1	13
β-strand	100-103	4	12
α-helix	107-109	3
β-strand	115	1	10
α-helix	116-118	3
β-strand	119-122	4	12
α-helix	124-131	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin-E9 immunity protein	A, E	protein	86	Escherichia coli K12	P13479 (AlphaFold model)
Colicin-E9	B, F	protein	134	Escherichia coli K12	P09883 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>2GYK_1 Colicin-E9 immunity protein (chains A, E)
MELKHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSALIYYPKEGD
DDSPSGIVNTVKQWRAANGKSGFKQG

Sequence of entity 2 (B, F), FASTA

>2GYK_2 Colicin-E9 (chains B, F)
MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEE
VSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIR
VTTPKRHIDIHRGK

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
ZN	Zinc ion	Zn	2

Primary citation

Crystal structures of the complexes of the Colicin E9 DNase domain with mutant immunity proteins. Kuhlmann, U.C., Santi, P.S., Kolade, O.O. et al. To be published.

Other PDB entries of the same protein (UniProt P13479 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FR2 1.6 Å, Crystal structure of the E9 DNase domain with a mutant immunity protein IM9(E41A)
2GZJ 1.6 Å, Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)
2VLN 1.6 Å, N75A mutant of E9 DNase domain in complex with Im9
2VLQ 1.6 Å, F86A mutant of E9 DNase domain in complex with Im9
1EMV 1.7 Å, Crystal structure of colicin E9 DNase domain with its cognate immunity protein IM9 (1.7 Å)
2GZG 1.7 Å, Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (Y55F)
2GZI 1.7 Å, Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (V34A)
2GZF 1.75 Å, Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y54F)
2GZE 1.8 Å, Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y55A)
2VLO 1.8 Å, K97A mutant of E9 DNase domain in complex with Im9
2VLP 2.0 Å, R54A mutant of E9 DNase domain in complex with Im9
1BXI 2.05 Å, Crystal structure of the escherichia coli colicin E9 DNase domain with its cognate…

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