Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.29 kDa 
• Atom Count: 1470 
• Modelled Residue Count: 153 
• Deposited Residue Count: 153 
• Unique protein chains: 1

1GDJ

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

• PDB DOI: 10.2210/pdb1GDJ/pdb
• Entry: 1GDJ supersedes: 1LH4, 2LH4

• Classification: OXYGEN TRANSPORT
• Organism(s): Lupinus luteus
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.165 

Literature

The Structure of Deoxy- and Oxy-Leghaemoglobin from Lupin

Harutyunyan, H.E., Safonova, T.N., Kuranova, I.P., Popov, A.N., Teplyakov, A.V., Obmolova, G.V., Rusakov, A.A., Vainshtein, B.K., Dodson, G.G., Wilson, J.C., Perutz, M.F.

(1995) J Mol Biol 251: 104-115

• PubMed: 7643380 
• DOI: 10.1006/jmbi.1995.0419
• Primary Citation of Related Structures:  
  1GDJ, 2GDM


• PubMed Abstract: 
  

The leghaemoglobins have oxygen affinities 11 to 24 times higher than that of sperm whale myoglobin, due mainly to higher rates of association. To find out why, we have determined the structures of deoxy- and oxy-leghaemoglobin II of the lupin at 1.7 A resolution. Results confirm the general features found in previous X-ray analyses of this protein. The unique feature that has now emerged is the rotational freedom of the proximal histidine. In deoxy-leghaemoglobin the imidazole oscillates between two alternative orientations, eclipsing either the lines N1-N3 or N2-N4 of the porphyrin; in oxy-leghaemoglobin it is fixed in a staggered orientation. The iron atom moves from a position 0.30 A from the plane of the pyrrole nitrogen atoms in deoxy- to a position in the plane in oxy-leghaemoglobin while the Fe- bond distance remains constant at 2.02 A. The Fe-O-O angle is 152 degrees, as in human haemoglobin. The oxygen is hydrogen-bonded to the distal histidine at N epsilon 2-O1 and N epsilon 2-O2 distance of 2.95 A and 2.68 A, respectively. The porphyrin is ruffled equally in deoxy- and oxy-leghaemoglobins, due to rotations of the pyrrols about the N-Fe-N bonds, causing the methine bridges to deviate by up to 0.32 A from the mean porphyrin plane. The only feature capable of accounting for the high on-rate of the reaction with oxygen are the mobilities of the proximal histidine and distal histidine residues in deoxy-leghaemoglobin. The eclipsed positions of the proximal histidine in deoxy-leghaemoglobin maximize steric hindrance with the porphyrin nitrogen atoms and minimize pi-->p electron donation, while its staggered position in oxy-leghaemoglobin reverses both these effects. Together with the oscillation of the imidazole between the two orientations, these two factors may reduce the activation energy for the reaction of leghaemoglobin with oxygen. The distal histidine is in a fixed position in the haem pocket in the crystal, but must be swinging in and out of the pocket at a high rate in solution to allow the oxygen to enter.

---

Related Citations: 

• Crystal Structure of Ferric Complexes of the Yellow Lupin Leghemoglobin with Isoquinoline at 1.8 Angstroms Resolution (Russian)
  Safonova, T.N., Teplyakov, A.V., Obmolova, G.V., Popov, A.N., Kuranova, I.P., Harutyunyan, E.G.
  (1991) Bioorg Khim 17: 1605

• 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

• 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) Кристаллография 25: 80

• 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 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) Кристаллография 23: 517

• 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

• 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 233: 67

• 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) Кристаллография 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

• 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

• 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 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

• 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) Кристаллография 19: 971

• 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) Кристаллография 19: 964

• 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 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 216: 226

• Cell Parameters of Crystalline Plant (Lupinus Luteus (Lupine)) Hemoglobin (Russian)
  Arutyunyan, E.G., Zaitsev, V.N., Zhiznevskaya, G.Ya., Borodenko, L.I.
  (1971) Кристаллография 16: 237

• 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

---

Organizational Affiliation: 

Institute of Crystallography, Russian Academy of Sciences, Moscow.

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.48	α = 90
b = 51.6	β = 98.8
c = 38.33	γ = 90

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.
• This entry supersedes: 1LH4, 2LH4

Revision History  

• Version 1.0: 1995-02-27
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-10-29
  Changes: Derived calculations
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other