5UX2 | pdb_00005ux2

Protein 19 with aldehyde deformylating oxidase activity from Synechococcus

• PDB DOI: https://doi.org/10.2210/pdb5UX2/pdb

• Classification: LYASE
• Organism(s): Synechococcus sp. RS9917
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-21 Released: 2018-02-28 
• Deposition Author(s): Wilson, D.K., Mak, W.S., Siegel, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Protein 19 with aldehyde deformylating oxidase activity from Synechococcus

Wilson, D.K., Mak, W.S., Siegel, J.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.94 kDa 
• Atom Count: 3,496 
• Modeled Residue Count: 438 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde decarbonylase	A, B	234	Synechococcus sp. RS9917	Mutation(s): 0  Gene Names: RS9917_12945 EC: 4.1.99.5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPI	E [auth A], H [auth B]	PROPANOIC ACID C3 H6 O2 XBDQKXXYIPTUBI-UHFFFAOYSA-N
FE	C [auth A], D [auth A], F [auth B], G [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.986	α = 90
b = 90.227	β = 90
c = 109.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Wilson, D.K., Mak, W.S., Siegel, J.B.

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description