4UII

Crystal structure of the Azotobacter vinelandii globin-coupled oxygen sensor in the aquo-met form

• PDB DOI: https://doi.org/10.2210/pdb4UII/pdb

• Classification: TRANSFERASE
• Organism(s): Azotobacter vinelandii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-30 Released: 2016-04-13 
• Deposition Author(s): Germani, F., De Schutter, A., Pesce, A., Berghmans, H., Van Hauwaert, M.-L., Cuypers, B., Bruno, S., Mozzarelli, A., Moens, L., Van Doorslaer, S., Bolognesi, M., Nardini, M., Dewilde, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.297 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 

Literature

Azotobacter Vinelandii Globin-Coupled Oxygen Sensor is a Diguanylate Cyclase with a Biphasic Oxygen Dissociation

Germani, F., De Schutter, A., Pesce, A., Berghmans, H., Van Hauwaert, M.-L., Cuypers, B., Bruno, S., Mozzarelli, A., Moens, L., Van Doorslaer, S., Bolognesi, M., Nardini, M., Dewilde, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.91 kDa 
• Atom Count: 2,186 
• Modelled Residue Count: 258 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF DOMAIN PROTEIN	A, B	217	Azotobacter vinelandii	Mutation(s): 0  EC: 2.7.7.65
UniProt
Find proteins for M9YE33 (Azotobacter vinelandii CA6) Explore M9YE33  Go to UniProtKB:  M9YE33

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.297 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.89	α = 90
b = 49.49	β = 91.81
c = 62.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Germani, F., De Schutter, A., Pesce, A., Berghmans, H., Van Hauwaert, M.-L., Cuypers, B., Bruno, S., Mozzarelli, A., Moens, L., Van Doorslaer, S., Bolognesi, M., Nardini, M., Dewilde, S.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description