5YM7

Crystal Structure of B562RIL without disulfide bond

• PDB DOI: https://doi.org/10.2210/pdb5YM7/pdb

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


• Deposited: 2017-10-21 Released: 2017-11-22 
• Deposition Author(s): Pu, M., Xu, Z., Song, G., Liu, Z.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.238 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

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 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: 11.79 kDa 
• Atom Count: 972 
• Modelled Residue Count: 106 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A	106	Escherichia coli	Mutation(s): 3  Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.238 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.847	α = 90
b = 51.155	β = 90
c = 89.95	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Pu, M., Xu, Z., Song, G., Liu, Z.J.

Revision History  

• Version 1.0: 2017-11-22
  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