4JEA: Soluble cytochrome b562

Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide bonds. Determined by X-ray diffraction at 1.22 Å resolution. Released 21 Aug 2013.

Method: X-ray diffraction
Resolution: 1.22 Å
Organism: Escherichia coli
Chains: 4
Atoms: 4,088
Mol. weight: 50.1 kDa
Ligands: ZN, HEM
Released: 21 Aug 2013

Explore 4JEA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JEA contains 20 α-helices and 0 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, C and D: 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

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-18	16
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, C, D	protein	106	Escherichia coli	P0ABE7 (AlphaFold model)

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

>4JEA_1 soluble cytochrome b562 (chains A, B, C, D)
ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHD
FRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4

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

Primary citation

In Vitro and Cellular Self-Assembly of a Zn-Binding Protein Cryptand via Templated Disulfide Bonds. Medina-Morales, A., Perez, A., Brodin, J.D. et al. J Am Chem Soc (2013) 135:12013-12022. DOI 10.1021/ja405318d · PubMed

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

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
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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