6DYF: Soluble cytochrome b562

Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y. Determined by X-ray diffraction at 1.1 Å resolution. Released 24 Apr 2019.

Method: X-ray diffraction
Resolution: 1.1 Å
Organism: Escherichia coli
Chains: 2
Atoms: 2,259
Mol. weight: 25.29 kDa
Ligands: HEC, CU
Released: 24 Apr 2019

Explore 6DYF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DYF contains 12 α-helices and 0 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	3-19	17
α-helix	23-40	18
α-helix	44-45	2
α-helix	46-48	3
α-helix	56-80	25
α-helix	84-92	9
α-helix	95-105	11

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-19	17
α-helix	23-40	18
α-helix	46-48	3
α-helix	56-80	25
α-helix	84-105	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562	A, B	protein	106	Escherichia coli	P0ABE7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6DYF_1 Soluble cytochrome b562 (chains A, B)
ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMWD
FRHGFDHLVYHIDDALKLANEGKVKEAQAAAEQLKCHCNACHQKYR

Ligands and cofactors

ID	Name	Formula	Copies
HEC	Heme C	C34 H36 Fe N4 O4	2
CU	Copper (II) ion	Cu	1

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

Primary citation

An efficient, step-economical strategy for the design of functional metalloproteins. Rittle, J., Field, M.J., Green, M.T. et al. Nat Chem (2019) 11:434-441. DOI 10.1038/s41557-019-0218-9 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y
6OT8 1.5 Å, Bimetallic hexameric cage design 4 (BMC4) from cytochrome cb562

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