1V15: Colicin E9, mutant HIS103ALA

Crystal structure of the colicin E9, mutant HIS103ALA, in complex with ZN+2 and dsDNA (resolution 2.4A). Determined by X-ray diffraction at 2.4 Å resolution. Released 23 Jun 2004.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: ESCHERICHIA COLI
Chains: 12
Atoms: 5,261
Mol. weight: 80.16 kDa
Ligands: ZN
Released: 23 Jun 2004

Explore 1V15 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1V15 contains 33 α-helices and 48 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.

Chain A: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	1
β-strand	32	1	2
α-helix	50-63	14
α-helix	77-81	5
α-helix	83-85	3
β-strand	86	1	3
α-helix	89-91	3
β-strand	93	1	4
β-strand	96	1	4
β-strand	98	1	3
β-strand	100-103	4	2
β-strand	115	1	1
β-strand	119-122	4	2
α-helix	124-130	7

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	5
β-strand	12	1	6
β-strand	16	1	7
α-helix	20-27	8
β-strand	32-33	2	8
α-helix	34	1
β-strand	35	1	7
α-helix	36-42	7
β-strand	46-47	2	5
α-helix	50-63	14
α-helix	65-67	3
α-helix	73-80	8
α-helix	83-85	3
β-strand	86	1	9
α-helix	87-88	2
α-helix	89-91	3
β-strand	93	1	10
β-strand	96	1	10
β-strand	98	1	9
β-strand	100-103	4	8
β-strand	115	1	6
β-strand	119-122	4	8
α-helix	124-132	9

Chain C: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	11
β-strand	12	1	12
β-strand	16	1	13
α-helix	25-27	3
β-strand	32	1	14
α-helix	33-34	2
β-strand	35	1	13
α-helix	36-42	7
β-strand	46-47	2	11
α-helix	50-63	14
α-helix	65-67	3
α-helix	73-80	8
α-helix	83-85	3
β-strand	86	1	15
α-helix	87-88	2
α-helix	89-91	3
β-strand	93	1	16
β-strand	96	1	16
β-strand	98	1	15
β-strand	100-103	4	14
β-strand	115	1	12
β-strand	119-122	4	14
α-helix	124-130	7

Chain D: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	17
β-strand	12	1	18
β-strand	16	1	19
α-helix	22-27	6
β-strand	32	1	20
β-strand	35	1	19
α-helix	36-42	7
β-strand	46-47	2	17
α-helix	50-63	14
α-helix	65-68	4
α-helix	73-80	8
α-helix	83-85	3
β-strand	86	1	21
α-helix	89-91	3
β-strand	93	1	22
β-strand	96	1	22
β-strand	98	1	21
β-strand	100-103	4	20
β-strand	115	1	18
β-strand	119-122	4	20
α-helix	124-132	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin E9	A, B, C, D	protein	134	ESCHERICHIA COLI	P09883 (AlphaFold model)
5'-d(gpcpgpaptpcpgpcp)-3'	E, F, G, H, I, J, K, L	DNA	8

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

>1V15_1 COLICIN E9 (chains A, B, C, D)
MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEE
VSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIR
VTTPKRHIDIHRGK

Sequence of entity 2 (E, F, G, H, I, J, K, L), FASTA

>1V15_2 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' (chains E, F, G, H, I, J, K, L)
GCGATCGC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases. Mate, M.J., Kleanthous, C. J Biol Chem (2004) 279:34763. DOI 10.1074/JBC.M403719200 · PubMed

Other PDB entries of the same protein (UniProt P09883 (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)
2GYK 1.6 Å, Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity…
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)
2WPT 1.78 Å, The crystal structure of Im2 in complex with colicin E9 DNase
1FSJ 1.8 Å, Crystal structure of the E9 DNase domain
2GZE 1.8 Å, Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y55A)

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