4Z5S

Crystal structure of apo-form of aldehyde deformylating oxygenase from Synechocystis sp.PCC 6803

• PDB DOI: https://doi.org/10.2210/pdb4Z5S/pdb

• Classification: LYASE
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-03 Released: 2016-04-06 
• Deposition Author(s): Jia, C., Li, M., Chang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.213 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Identification of residues important for the activity of aldehyde-deformylating oxygenase through investigation into the structure-activity relationship

Wang, Q., Bao, L., Jia, C., Li, M., Li, J.J., Lu, X.

(2017) BMC Biotechnol 17: 31-31

• PubMed: 28302170 
• DOI: https://doi.org/10.1186/s12896-017-0351-8
• Primary Citation of Related Structures:  
  4Z5S


• PubMed Abstract: 
  

  Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in the biosynthetic pathway of fatty alk(a/e)nes in cyanobacteria. However, cADO (cyanobacterial ADO) showed extreme low activity with the k _cat value below 1 min ^-1 , which would limit its application in biofuel production. To identify the activity related key residues of cADO is urgently required.

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Organizational Affiliation: 

Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.2 kDa 
• Atom Count: 2,112 
• Modelled Residue Count: 223 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde decarbonylase	A	231	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: sll0208 EC: 4.1.99.5
UniProt
Find proteins for Q55688 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q55688  Go to UniProtKB:  Q55688

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.213 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.519	α = 90
b = 88.027	β = 90
c = 36.251	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
ADSC	data collection
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Jia, C., Li, M., Chang, W.

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2017-04-05
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description