5YO3

Crystal Structure of B562RIL with engineered disulfide bond V16C-A29C

• PDB DOI: https://doi.org/10.2210/pdb5YO3/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-26 Released: 2018-05-09 
• Deposition Author(s): Pu, M., Xu, Z., Song, G., Liu, Z.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.188 
• R-Value Work: 0.155 
• R-Value Observed: 0.158 

Literature

Protein crystal quality oriented disulfide bond engineering.

Pu, M., Xu, Z., Peng, Y., Hou, Y., Liu, D., Wang, Y., Liu, H., Song, G., Liu, Z.J.

(2018) Protein Cell 9: 659-663

• PubMed: 29039033 
• DOI: https://doi.org/10.1007/s13238-017-0482-7
• Primary Citation of Related Structures:  
  5YM7, 5YO3, 5YO4, 5YO5, 5YO6, 5YOB, 5YOC, 5YOE, 5YOG

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.29 kDa 
• Atom Count: 1,069 
• Modelled Residue Count: 107 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A	107	Escherichia coli	Mutation(s): 5  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
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.188 
• R-Value Work: 0.155 
• R-Value Observed: 0.158 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.328	α = 90
b = 50.126	β = 90
c = 94.237	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Pu, M., Xu, Z., Song, G., Liu, Z.J.

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2018-07-11
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description