Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17318.57 
• Atom Count: 1222 
• Residue Count: 153 
• Unique protein chains: 1

1GDI

CRYSTAL STRUCTURE OF FERRIC COMPLEXES OF THE YELLOW LUPIN LEGHEMOGLOBIN WITH ISOQUINOLINE AT 1.8 ANGSTROMS RESOLUTION (RUSSIAN)

• DOI: 10.2210/pdb1GDI/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Lupinus luteus


• Deposited: 1994-09-14 Released: 1995-02-27 
• Deposition Author(s): Harutyunyan, E., Safonova, T., Kuranova, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å

Literature

The binding of carbon monoxide and nitric oxide to leghaemoglobin in comparison with other haemoglobins.

Harutyunyan, E.H., Safonova, T.N., Kuranova, I.P., Popov, A.N., Teplyakov, A.V., Obmolova, G.V., Valnshtein, B.K., Dodson, G.G., Wilson, J.C.

(1996) J.Mol.Biol. 264: 152-161

• PubMed: 8950274 
• Primary Citation of Related Structures:  
  1GDL


• PubMed Abstract: 
  

Haemoglobins have the ability to discriminate between oxygen and other diatomic molecules. To further understanding of this process the X-ray crystal structures of carbonmonoxy and nitrosyl-leghaemoglobin have been determined at 1.8 A resolution. The ligand geometry is discussed in detail and the controversial issue of bent versus linear carbon monoxide binding is addressed. The bond angle of 160 degrees for CO-leghaemoglobin is in conflict with recent spectroscopy results on myoglobin but is consistent with angles obtained for myoglobin X-ray crystal structures. In contrast to the numerous carbon monoxide studies, very little stereochemical information is available for the nitric oxide adduct of haemoglobin. This is provided by the X-ray structure of NO-leghaemoglobin, which conforms to expected geometry with an Fe-NO angle of 147 degrees and a lengthened iron-proximal histidine bond. Thus crystallographic evidence is given for the predicted weakening of this bond on the binding of nitric oxide.

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Related Citations: 

• X-Ray Structural Investigation of Leghemoglobin. Vi. Structure of Acetate-Ferrileghemoglobin at a Resolution of 2.0 Angstroms
  Arutyunyan, E.G.,Kuranova, I.P.,Vainshtein, B.K.,Steigemann, W.
  (1980) Sov.Phys.Crystallogr.(Engl.Transl.) 25: 43
• X-Ray Diffraction Determination of the Three-Dimensional Structure of Leghemoglobin of Lupinus Luteus L. With 5 Angstroms Resolution
  Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
  (1974) Dokl.Biochem.(Engl.Transl.) 216: 226
• X-Ray Structural Study of Leghemoglobin. III. Crystallographic Data on the Structure of the First Component (Russian)
  Arutyunyan, E.G.,Kuranova, I.P.,Grebenko, A.I.,Voronova, A.A.
  (1977) Kristallografiya 22: 634
• X-Ray Structural Study of Leghemoglobin. III. Crystallographic Data Regarding the Structure of the First Component
  Arutyunyan, E.G.,Kuranova, I.P.,Grebenko, A.I.,Voronova, A.A.
  (1977) Sov.Phys.Crystallogr.(Engl.Transl.) 22: 362
• Cell Parameters of Crystalline Plant (Lupinus Luteus (Lupine)) Hemoglobin (Russian)
  Arutyunyan, E.G.,Zaitsev, V.N.,Zhiznevskaya, G.Ya.,Borodenko, L.I.
  (1971) Kristallografiya 16: 237
• The X-Ray Structural Study of Leghemoglobin. I. Purification, Crystallization, and Production of Derivatives Containing Heavy Atoms (Russian)
  Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
  (1974) Kristallografiya 19: 964
• The X-Ray Structural Study of Leghemoglobin. II. Determination of the Structure at 5 Angstroms Resolution (Russian)
  Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
  (1974) Kristallografiya 19: 971
• The Haem-Accessibility in Leghaemoglobin of Lupinus Luteus as Observed by Proton Magnetic Relaxation
  Vuk-Pavlovic, S.,Benko, B.,Maricic, S.,Lahajnar, G.,Kuranova, I.P.,Vainshtein, B.K.
  (1976) Int.J.Pept.Protein Res. 8: 427
• Unit-Cell Parameters of Crystalline Plant Hemoglobin
  Arutyunyan, E.G.,Zaitsev, V.N.,Zhiznevskaya, G.Ya.,Borodenko, L.I.
  (1971) Sov.Phys.Crystallogr.(Engl.Transl.) 16: 193
• X-Ray Structural Investigation of Leghemoglobin. Iv. Structure Determination at a Resolution of 2.8 Angstroms
  Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Nekrasov, Yu.V.
  (1978) Sov.Phys.Crystallogr.(Engl.Transl.) 23: 287
• X-Ray Study of Leghemoglobin. I.Purification, Crystallization, and Preparation of Derivatives Containing Heavy Atoms
  Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
  (1975) Sov.Phys.Crystallogr.(Engl.Transl.) 19: 598
• Structure of Leghaemoglobin from Lupin Root Nodules at 5 Angstroms Resolution
  Vainshtein, B.K.,Harutyunyan, E.H.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovsky, A.G.,Grebenko, A.I.,Konareva, N.V.
  (1975) Nature 254: 163
• X-Ray Diffraction Study of Leghemoglobin. Iv. Determination of the Structure with 2.8 Angstroms Resolution (Russian)
  Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Nekrasov, Yu.V.
  (1978) Kristallografiya 23: 517
• X-Ray Study of Leghemoglobin. II. Determination of the Structure with Resolution of 5 Angstroms
  Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
  (1975) Sov.Phys.Crystallogr.(Engl.Transl.) 19: 602
• X-Ray Determination of Three-Dimensional Structure of Leghemoglobin from Lupinus Luteus L. At 5 Angstroms Resolution (Russian)
  Vainshtein, B.K.,Arutiunian, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
  (1974) Dokl.Akad.Nauk Sssr 216: 690
• X-Ray Structural Investigation of Leghemoglobin. Vi. Structure of Acetate-Ferrileghemoglobin at a Resolution of 2.0 Angstroms (Russian)
  Arutyunyan, E.G.,Kuranova, I.P.,Vainshtein, B.K.,Steigemann, W.
  (1980) Kristallografiya 25: 80
• Spatial Structure of Lupine Leghemoglobin with the 2.8 Angstroms Resolution (Russian)
  Vainshtein, B.K.,Arutiunian, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.,Nekrasov, Iu.V.
  (1977) Dokl.Akad.Nauk Sssr 233: 238
• Three-Dimensional Structure of Lupine Leghemoglobin with a Resolution of 2.8 Angstroms
  Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.,Nekrasov, Yu.V.
  (1977) Dokl.Biochem.(Engl.Transl.) 233: 67
• X-Ray Structure of Ferrous Complexes of the Yellow Lupin Leghemoglobin with Co and No at 1.8 Angstroms Resolution (Russian)
  Obmolova, G.V.,Safonova, T.N.,Teplyakov, A.V.,Popov, A.N.,Kuranova, I.P.,Harutyunyan, E.G.,Vainshtein, B.K.
  (1988) Bioorg.Khim. 14: 1509




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Organizational Affiliation: 

Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LEGHEMOGLOBIN (CARBONMONOXY)	A	153	Lupinus luteus	Mutation(s): 0
Find proteins for P02240 (Lupinus luteus) Go to UniProtKB:  P02240

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	A	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 93.190	α = 90.00
b = 51.950	β = 98.80
c = 38.300	γ = 90.00

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-09-14 
• Released Date: 1995-02-27 
• Deposition Author(s): Harutyunyan, E., Safonova, T., Kuranova, I.

Revision History 

• Version 1.0: 1995-02-27
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2014-10-22
  Type: Derived calculations
• Version 1.4: 2017-11-29
  Type: Derived calculations, Other