3ZFK: Colicin-E7

N-terminal truncated Nuclease Domain of Colicin E7. Determined by X-ray diffraction at 1.7 Å resolution. Released 18 Dec 2013.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: ESCHERICHIA COLI
Chains: 2
Atoms: 2,334
Mol. weight: 31.81 kDa
Ligands: ZN
Released: 18 Dec 2013

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

Secondary structure: helices and β-sheets

3ZFK contains 23 α-helices and 26 β-strands across 2 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: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	451-452	2	1
β-strand	454	1	2
β-strand	458	1	3
β-strand	474-475	2	4
α-helix	476	1
β-strand	477	1	3
α-helix	478-484	7
β-strand	488-489	2	1
α-helix	492-504	13
α-helix	507-510	4
α-helix	515-522	8
α-helix	525-527	3
β-strand	528	1	5
α-helix	529-530	2
α-helix	531-533	3
β-strand	535	1	6
β-strand	538	1	6
β-strand	540	1	5
β-strand	542-545	4	4
α-helix	549-551	3
β-strand	557	1	2
α-helix	558-560	3
β-strand	561-564	4	4
α-helix	566-572	7

Chain B: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	451-452	2	7
β-strand	454	1	8
β-strand	458	1	9
α-helix	464-467	4
β-strand	474-475	2	10
α-helix	476	1
β-strand	477	1	9
α-helix	478-484	7
β-strand	488-489	2	7
α-helix	492-505	14
α-helix	507-510	4
α-helix	515-522	8
α-helix	525-527	3
β-strand	528	1	11
α-helix	529-530	2
α-helix	531-533	3
β-strand	535	1	12
β-strand	538	1	12
β-strand	540	1	11
β-strand	542-545	4	10
α-helix	549-551	3
β-strand	557	1	8
α-helix	558-560	3
β-strand	561-564	4	10
α-helix	566-572	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin-E7	A, B	protein	135	ESCHERICHIA COLI	Q47112 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3ZFK_1 COLICIN-E7 (chains A, B)
GPLGSPEFPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWE
EVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNI
SVVTPKRHIDIHQVN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (ACT, SO4, CL) are not listed.

Primary citation

A New Insight Into the Zinc-Dependent DNA-Cleavage by the Colicin E7 Nuclease: A Crystallographic and Computational Study. Czene, A., Toth, E., Nemeth, E. et al. Metallomics (2014) 6:2090. DOI 10.1039/C4MT00195H · PubMed

Other PDB entries of the same protein (UniProt Q47112 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2AXC 1.7 Å, Crystal structure of ColE7 translocation domain
2JB0 1.91 Å, Crystal structure of the mutant H573A of the nuclease domain of COLE7 in complex with IM7
1MZ8 2.0 Å, Crystal structures of the nuclease domain of COLE7/IM7 in complex with a phosphate ion…
1ZNV 2.0 Å, How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal…
2ERH 2.0 Å, Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7…
2JAZ 2.03 Å, Crystal structure of the mutant N560D of the nuclease domain of COLE7 in complex with IM7
1M08 2.1 Å, Crystal structure of the unbound nuclease domain of ColE7
1UJZ 2.1 Å, Crystal structure of the E7_C/Im7_C complex; a computationally designed interface…
2JBG 2.2 Å, crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7
3GKL 2.2 Å, Following evolutionary paths to high affinity and selectivity protein-protein…
7CEI 2.3 Å, The endonuclease domain of colicin E7 in complex with its inhibitor IM7 protein
3GJN 2.48 Å, Following evolutionary paths to high affinity and selectivity protein-protein…

Browse structure collections

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