3TFG

Crystal structure of an H-NOX protein from Nostoc sp. PCC 7120, L66W/L67W double mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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 U S A 108: E881-E889

  • DOI: 10.1073/pnas.1114038108
  • Primary Citation of Related Structures:  
    3TFA, 3TFD, 3TF8, 3TF9, 3TF0, 3TF1, 3TFE, 3TFF, 3TFG

  • 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 highlighted the importance of gas pockets around the heme in controlling the capture and release of O(2) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alr2278 proteinA, B189Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 2 
Gene Names: alr2278
UniProt
Find proteins for Q8YUQ7 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YUQ7 
Go to UniProtKB:  Q8YUQ7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MLA
Query on MLA

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.123α = 90
b = 123.123β = 90
c = 123.123γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Non-polymer description