3WFW

Crystal Structure of the Closed Form of the HGbRL's Globin Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Open and Lys-His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites.

Teh, A.H.Saito, J.A.Najimudin, N.Alam, M.

(2015) Sci Rep 5: 11407-11407

  • DOI: 10.1038/srep11407
  • Primary Citation of Related Structures:  
    3WFW, 3WFX

  • PubMed Abstract: 
  • Globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. A putative globin-coupled sensor from Methylacidiphilum infernorum, HGbRL, contains an N-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture ...

    Globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. A putative globin-coupled sensor from Methylacidiphilum infernorum, HGbRL, contains an N-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture. Helices E and F fuse into an elongated helix, resulting in a novel site-swapped globin fold made up of helices A-E, hence the distal site, from one subunit and helices F-H, the proximal site, from another. The open structure possesses a large cavity binding an imidazole molecule, while the closed structure forms a unique Lys-His hexacoordinated species, with the first turn of helix E unravelling to allow Lys52(E10) to bind to the haem. Ligand binding induces reorganization of loop CE, which is stabilized in the closed form, and helix E, triggering a large conformational movement in the open form. These provide a mechanical insight into how a signal may be relayed between the globin domain and the C-terminal domain of HGbRL, a Roadblock/LC7 domain. Comparison with HGbI, a closely related globin, further underlines the high degree of structural versatility that the globin fold is capable of, enabling it to perform a diversity of functions.


    Organizational Affiliation

    1] Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Honolulu, HI 96822, United States [2] Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Honolulu, HI 96822, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain A138Methylacidiphilum infernorum V4Mutation(s): 0 
Gene Names: hmpMinf_1089
Find proteins for B3DUZ1 (Methylacidiphilum infernorum (isolate V4))
Explore B3DUZ1 
Go to UniProtKB:  B3DUZ1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.24α = 90
b = 54.4β = 106.17
c = 44.71γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-07-24 
  • Released Date: 2014-08-06 
  • Deposition Author(s): Teh, A.H.

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references, Derived calculations