2OIF

The crystal structure of ferric cyanide bound barley hexacoordinate hemoglobin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Plant hemoglobins: a molecular fossil record for the evolution of oxygen transport

Hoy, J.A.Robinson, H.Trent III, J.T.Kakar, S.Smagghe, B.J.Hargrove, M.S.

(2007) J Mol Biol 371: 168-179

  • DOI: https://doi.org/10.1016/j.jmb.2007.05.029
  • Primary Citation of Related Structures:  
    2OIF

  • PubMed Abstract: 

    The evolution of oxygen transport hemoglobins occurred on at least two independent occasions. The earliest event led to myoglobin and red blood cell hemoglobin in animals. In plants, oxygen transport "leghemoglobins" evolved much more recently. In both events, pentacoordinate heme sites capable of inert oxygen transfer evolved from hexacoordinate hemoglobins that have unrelated functions. High sequence homology between hexacoordinate and pentacoordinate hemoglobins in plants has poised them for potential structural analysis leading to a molecular understanding of this important evolutionary event. However, the lack of a plant hexacoordinate hemoglobin structure in the exogenously ligand-bound form has prevented such comparison. Here we report the crystal structure of the cyanide-bound hexacoordinate hemoglobin from barley. This presents the first opportunity to examine conformational changes in plant hexacoordinate hemoglobins upon exogenous ligand binding, and reveals structural mechanisms for stabilizing the high-energy pentacoordinate heme conformation critical to the evolution of reversible oxygen binding hemoglobins.


  • Organizational Affiliation

    Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-legume hemoglobin
A, B, C, D, E
A, B, C, D, E, F, G, H
162Hordeum vulgareMutation(s): 0 
Gene Names: HBGLB1
UniProt
Find proteins for Q42831 (Hordeum vulgare)
Explore Q42831 
Go to UniProtKB:  Q42831
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42831
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
CA [auth F]
FA [auth G]
IA [auth H]
J [auth A]
O [auth B]
CA [auth F],
FA [auth G],
IA [auth H],
J [auth A],
O [auth B],
R [auth C],
U [auth D],
Y [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PGO
Query on PGO

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
GA [auth G]
JA [auth H]
K [auth A]
AA [auth E],
DA [auth F],
GA [auth G],
JA [auth H],
K [auth A],
KA [auth H],
L [auth A],
M [auth A],
P [auth B],
S [auth C],
V [auth D],
W [auth D],
Z [auth E]
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
CYN
Query on CYN

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
HA [auth H]
I [auth A]
N [auth B]
BA [auth F],
EA [auth G],
HA [auth H],
I [auth A],
N [auth B],
Q [auth C],
T [auth D],
X [auth E]
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.74α = 99.17
b = 60.557β = 96.97
c = 145.804γ = 92.43
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2007-07-24 
  • Deposition Author(s): Hoy, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-19
    Changes: Advisory, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations