Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.42 kDa 
• Atom Count: 869 
• Modelled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

1QPU

SOLUTION STRUCTURE OF OXIDIZED ESCHERICHIA COLI CYTOCHROME B562

• PDB DOI: 10.2210/pdb1QPU/pdb
• BMRB: 4759

• Classification: ELECTRON TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-05-30 Released: 1999-06-02 
• Deposition Author(s): Arnesano, F., Banci, L., Bertini, I., Faraone-Mennella, J., Rosato, A., Barker, P.D., Fersht, A.R.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

The solution structure of oxidized Escherichia coli cytochrome b562.

Arnesano, F., Banci, L., Bertini, I., Faraone-Mennella, J., Rosato, A., Barker, P.D., Fersht, A.R.

(1999) Biochemistry 38: 8657-8670

• PubMed: 10393541 
• DOI: 10.1021/bi982785f
• Primary Citation of Related Structures:  
  1QPU


• PubMed Abstract: 
  

The solution structure of the oxidized, paramagnetic form of cytochrome b562 from Escherichia coli (106 amino acids) is here reported as obtained from 1653 meaningful NOEs (from a total of 2051 unique NOEs), 33 (3)JHNHalpha values, and 339 pseudocontact shifts. The structure displays the typical four-helix bundle motif, and a disordered loop between helices alpha2 and alpha3, as found in the solid state. The solution structure has a conformation intermediate between the two independent solid-state molecules, although different orientations are observed for a few residues. The magnetic susceptibility tensor is similar to that of cytochrome c, which has the same ligands, although the anisotropy is somewhat smaller. This difference in the electronic structure is consistent with the thermal accessibility in cytochrome b562 of states with S > 1/2. The structure is also compared with the solution structure of the apoprotein, and some information on the role of the cofactor on the protein folding and mobility is obtained. Helix alpha4 seems to be the most sensitive to the chemical environment in terms of structure and mobility. The pKa values affecting the hyperfine-shifted signals are also discussed. Quite intriguing is the comparison of the structure of cytochrome b562 with the available structures of cytochromes c' which display a similar folding motif and similar pKa values but very little sequence similarity.

---

Organizational Affiliation: 

Department of Chemistry, Centro di Risonanze Magnetiche, University of Florence, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME B562	A	106	Escherichia coli	Mutation(s): 0  Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• OLDERADO: 1QPU Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-30 
• Released Date: 1999-06-02 
Deposition Author(s): Arnesano, F., Banci, L., Bertini, I., Faraone-Mennella, J., Rosato, A., Barker, P.D., Fersht, A.R.

Revision History  

• Version 1.0: 1999-06-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations