5YO3 | pdb_00005yo3

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 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

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 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.
iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Insititute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, 650500, China.
Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, China.
Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, China. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
Insititute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, 650500, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [e-mail].

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 
• Modeled 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 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

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
• Version 1.3: 2024-10-09
  Changes: Structure summary