3FBD: Nuclease domain of COLE7(D493Q mutant)

Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA. Determined by X-ray diffraction at 2.9 Å resolution. Released 3 Nov 2009.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Escherichia coli
Chains: 6
Atoms: 3,663
Mol. weight: 52.39 kDa
Released: 3 Nov 2009

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

Secondary structure: helices and β-sheets

3FBD contains 19 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: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	451-452	2	1
β-strand	454	1	2
β-strand	458	1	3
α-helix	465-467	3
β-strand	474-475	2	4
β-strand	477	1	3
α-helix	478-484	7
β-strand	488-489	2	1
α-helix	492-505	14
α-helix	507-510	4
α-helix	515-521	7
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
β-strand	561-564	4	4
α-helix	566-572	7

Chain D: 9 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	464-468	5
β-strand	474-475	2	10
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	515-521	7
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
β-strand	557	1	8
β-strand	561-564	4	10
α-helix	566-572	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin-E7	A, D	protein	132	Escherichia coli	Q47112 (AlphaFold model)
5'-d(dgpdgpdapdapdtpdtpdcpdgpdapdtpdcpdgpdapdapdtpdtpdcpdc)-3'	B, C, E, F	DNA	18

Sequence of entity 1 (A, D), FASTA

>3FBD_1 Colicin-E7 (chains A, D)
SKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFQDFRKKFWEEVS
KDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVV
TPKRHIDIHRGK

Sequence of entity 2 (B, C, E, F), FASTA

>3FBD_2 5'-D(*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DAP*DTP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*DC)-3' (chains B, C, E, F)
GGAATTCGATCGAATTCC

Primary citation

Redesign of high-affinity nonspecific nucleases with altered sequence preference. Wang, Y.T., Wright, J.D., Doudeva, L.G. et al. To be published.

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
3ZFK 1.7 Å, N-terminal truncated Nuclease Domain of Colicin E7
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

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