2BK9

Drosophila Melanogaster globin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.101 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CG9734-PA
A
153Drosophila melanogasterMutation(s): 1 
Gene Names: glob1 (DmeGb1, DmeGlob1, dmeglob1, Dmel\CG9734, DmHb, DmHb1, Glob1, globin1, Hb)
Find proteins for Q9VF15 (Drosophila melanogaster)
Go to UniProtKB:  Q9VF15
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CXS
Query on CXS

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

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

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.101 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.752α = 90.00
b = 55.835β = 90.00
c = 56.163γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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