5UXG | pdb_00005uxg

Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)

• PDB DOI: https://doi.org/10.2210/pdb5UXG/pdb

• Classification: LYASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-22 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: 1.72 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: in silico

Literature

Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)

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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.12 kDa 
• Atom Count: 3,741 
• Modeled Residue Count: 423 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aldehyde deformylating oxygenase	A, B	220	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: ST1620, STK_16200
UniProt
Find proteins for Q970H5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970H5  Go to UniProtKB:  Q970H5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.536	α = 90
b = 64.849	β = 116.86
c = 71.299	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: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description