2BK9

Drosophila Melanogaster globin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.102 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bishistidyl Heme Hexacoordination, a Key Structural Property in Drosophila Melanogaster Hemoglobin

De Sanctis, D.Dewilde, S.Vonrhein, C.Pesce, A.Moens, L.Ascenzi, P.Hankeln, T.Burmester, T.Ponassi, M.Nardini, M.Bolognesi, M.

(2005) J Biol Chem 280: 27222

  • DOI: 10.1074/jbc.M503814200
  • Primary Citation of Related Structures:  
    2BK9

  • PubMed Abstract: 
  • Hemoglobins at high concentration have been isolated long ago from some insect larvae living in hypoxic environments. Conversely, a monomeric hemoglobin has been discovered recently in the fruit fly Drosophila melanogaster as intracellular protein ex ...

    Hemoglobins at high concentration have been isolated long ago from some insect larvae living in hypoxic environments. Conversely, a monomeric hemoglobin has been discovered recently in the fruit fly Drosophila melanogaster as intracellular protein expressed both in larvae and in the adult fly. Such a finding indicates that the oxygen supply in insects may be more complex than previously thought, relying not only on O2 diffusion through the tubular tracheal system, but also on carrier-mediated transport and storage. We present here the crystal structure of recombinant D. melanogaster hemoglobin at 1.20 A resolution. Spectroscopic data show that the protein displays a hexacoordinated heme, whose axial ligands are the proximal and distal His residues. Such bis-His ligation of the heme has sizable effects on the protein local structure. Three protein matrix cavities, comparable in size but not in topological locations with those of sperm whale myoglobin, are spread through the protein matrix; one of these can host a xenon atom. Additionally, D. melanogaster hemoglobin binds one molecule of 3-(cyclohexylamino)propanesulfonic acid (CAPS) buffer at a surface pocket, next to the EF hinge. Despite the high resolution achieved, no sequence/structure features specifically supporting the heme hexa- to pentacoordination transition required for diatomic ligand binding could be recognized.


    Organizational Affiliation

    Department of Physics, National Institute for the Physics of Matter (NFM), University of Genova, Genova I-16146, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CG9734-PAA153Drosophila melanogasterMutation(s): 1 
Gene Names: 
EC: 1.11.1.7
Find proteins for Q9VF15 (Drosophila melanogaster)
Explore Q9VF15 
Go to UniProtKB:  Q9VF15
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Download CCD File 
A
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.102 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.752α = 90
b = 55.835β = 90
c = 56.163γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-20
    Type: Initial release
  • Version 1.1: 2013-02-06
    Changes: Atomic model, Non-polymer description, Version format compliance