3TFA

Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120 under 6 atm of xenon

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2711 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain.

Winter, M.B., Herzik, M.A., Kuriyan, J., Marletta, M.A.

(2011) Proc.Natl.Acad.Sci.USA 108: E881-E889

  • DOI: 10.1073/pnas.1114038108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Interior topological features, such as pockets and channels, have evolved in proteins to regulate biological functions by facilitating the diffusion of biomolecules. Decades of research using the globins as model heme proteins have clearly highlighte ...

    Interior topological features, such as pockets and channels, have evolved in proteins to regulate biological functions by facilitating the diffusion of biomolecules. Decades of research using the globins as model heme proteins have clearly highlighted the importance of gas pockets around the heme in controlling the capture and release of O(2). However, much less is known about how ligand migration contributes to the diverse functions of other heme protein scaffolds. Heme nitric oxide/oxygen binding (H-NOX) domains are a conserved family of gas-sensing heme proteins with a divergent fold that are critical to numerous signaling pathways. Utilizing X-ray crystallography with xenon, a tunnel network has been shown to serve as a molecular pathway for ligand diffusion. Structure-guided mutagenesis results show that the tunnels have unexpected effects on gas-sensing properties in H-NOX domains. The findings provide insights on how the flux of biomolecules through protein scaffolds modulates protein chemistry.

    Organizational Affiliation: 

    Department of Chemistry, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alr2278 protein
A, B
189Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 0 
Find proteins for Q8YUQ7 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  Q8YUQ7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
XE
Query on XE
Download SDF File 
Download CCD File 
A, B
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2711 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.163 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 123.937α = 90.00
b = 123.937β = 90.00
c = 123.937γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-09
    Type: Initial release