1XBN | pdb_00001xbn

Crystal structure of a bacterial nitric oxide sensor: an ortholog of mammalian soluble guanylate cyclase heme domain

• PDB DOI: https://doi.org/10.2210/pdb1XBN/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-30 Released: 2004-09-07 
• Deposition Author(s): Nioche, P., Raman, C.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.291 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.265 (Depositor) 

Literature

Femtomolar sensitivity of a NO sensor from Clostridium botulinum

Nioche, P., Berka, V., Vipond, J., Minton, N., Tsai, A.-L., Raman, C.S.

(2004) Science 306: 1550-1553

• PubMed: 15472039 
• DOI: https://doi.org/10.1126/science.1103596
• Primary Citation Related Structures: 
  1XBN


• PubMed Abstract: 
  

  Nitric oxide (NO) is extremely toxic to Clostridium botulinum, but its molecular targets are unknown. Here, we identify a heme protein sensor (SONO) that displays femtomolar affinity for NO. The crystal structure of the SONO heme domain reveals a previously undescribed fold and a strategically placed tyrosine residue that modulates heme-nitrosyl coordination. Furthermore, the domain architecture of a SONO ortholog cloned from Chlamydomonas reinhardtii indicates that NO signaling through cyclic guanosine monophosphate arose before the origin of multicellular eukaryotes. Our findings have broad implications for understanding bacterial responses to NO, as well as for the activation of mammalian NO-sensitive guanylyl cyclase.

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Organizational Affiliation: 
• Structural Biology Research Center and Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.5 kDa 
• Atom Count: 1,665 
• Modeled Residue Count: 195 
• Deposited Residue Count: 195 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-accepting chemotaxis protein	A	195	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 0  Gene Names: Tar4
UniProt
Find proteins for Q8RBX6 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RBX6  Go to UniProtKB:  Q8RBX6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OXY	B [auth A]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.291 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.265 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/91

Diffraction Data: https://doi.org/10.15785/SBGRID/96

Diffraction Data: https://doi.org/10.15785/SBGRID/97

Space Group: P 4₂ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.607	α = 90
b = 120.607	β = 90
c = 120.607	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-07 
Deposition Author(s): Nioche, P., Raman, C.S.

Revision History  

• Version 1.0: 2004-09-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations