4UIQ | pdb_00004uiq

Isolated globin domain of the Bordetella pertussis globin-coupled sensor with a heme at the dimer interface

• PDB DOI: https://doi.org/10.2210/pdb4UIQ/pdb

• Classification: TRANSFERASE
• Organism(s): Bordetella pertussis Tohama I
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-03-31 Released: 2016-04-13 
• Deposition Author(s): Germani, F., Donne, J., De Schutter, A., Pesce, A., Berghmans, H., Van Hauwaert, M.-L., Moens, L., Van Doorslaer, S., Bolognesi, M., Nardini, M., Dewilde, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.204 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Identification of a Putative Allosteric Site in the Sensor Domain of Bordetella Pertussis Globin- Coupled Sensor for the Control of Biofilm Formation

Germani, F., Donne, J., De Schutter, A., Pesce, A., Berghmans, H., Van Hauwaert, M.-L., 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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 42.65 kDa 
• Atom Count: 2,855 
• Modeled Residue Count: 307 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLOBIN-COUPLED SENSOR WITH DIGUANYLATE CYCLASE ACTIVITY	A, B	177	Bordetella pertussis Tohama I	Mutation(s): 4  EC: 2.7.7.65
UniProt
Find proteins for Q7VTL8 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VTL8  Go to UniProtKB:  Q7VTL8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth A], G [auth B], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	I [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.204 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.96	α = 90
b = 53.11	β = 93.23
c = 81.17	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Germani, F., Donne, J., De Schutter, A., Pesce, A., Berghmans, H., Van Hauwaert, M.-L., 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: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary