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Open data
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Basic information
Entry | Database: PDB / ID: 2gdm | |||||||||
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Title | LEGHEMOGLOBIN (OXY) | |||||||||
![]() | LEGHEMOGLOBIN (OXY) | |||||||||
![]() | OXYGEN TRANSPORT / LEGHEMOGLOBIN / LUPINE | |||||||||
Function / homology | ![]() response to nitrate / oxygen carrier activity / oxygen binding / heme binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Harutyunyan, E.H. / Safonova, T.N. / Kuranova, I.P. / Popov, A.N. / Teplyakov, A.V. / Obmolova, G.V. / Rusakov, A.A. / Dodson, G.G. / Wilson, J.C. / Perutz, M.F. | |||||||||
![]() | ![]() Title: The Structure of Deoxy-and Oxy-Leghaemoglobin from Lupin Authors: 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. #1: ![]() Title: Crystal Structure of Ferric Complexes of the Yellow Lupin Leghemoglobin with Isoquinoline at 1.8 Angstroms Resolution (Russian) Authors: Safonova, T.N. / Teplyakov, A.V. / Obmolova, G.V. / Popov, A.N. / Kuranova, I.P. / Harutyunyan, E.G. #2: ![]() Title: X-Ray Structure of Ferrous Complexes of the Yellow Lupin Leghemoglobin with Co and No at 1.8 Angstroms Resolution (Russian) Authors: Obmolova, G.V. / Safonova, T.N. / Teplyakov, A.V. / Popov, A.N. / Kuranova, I.P. / Harutyunyan, E.G. / Vainshtein, B.K. #3: ![]() Title: X-Ray Structural Investigation of Leghemoglobin. Vi. Structure of Acetate-Ferrileghemoglobin at a Resolution of 2.0 Angstroms (Russian) Authors: Arutyunyan, E.G. / Kuranova, I.P. / Vainshtein, B.K. / Steigemann, W. #4: ![]() Title: X-Ray Structural Investigation of Leghemoglobin. Vi. Structure of Acetate-Ferrileghemoglobin at a Resolution of 2.0 Angstroms Authors: Arutyunyan, E.G. / Kuranova, I.P. / Vainshtein, B.K. / Steigemann, W. #5: ![]() Title: X-Ray Diffraction Study of Leghemoglobin. Iv. Determination of the Structure with 2.8 Angstroms Resolution (Russian) Authors: Vainshtein, B.K. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Nekrasov, Yu.V. #6: ![]() Title: X-Ray Structural Investigation of Leghemoglobin. Iv. Structure Determination at a Resolution of 2.8 Angstroms Authors: Vainshtein, B.K. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Nekrasov, Yu.V. #7: ![]() Title: Three-Dimensional Structure of Lupine Leghemoglobin with a Resolution of 2.8 Angstroms Authors: 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. #8: ![]() Title: X-Ray Structural Study of Leghemoglobin. III. Crystallographic Data on the Structure of the First Component (Russian) Authors: Arutyunyan, E.G. / Kuranova, I.P. / Grebenko, A.I. / Voronova, A.A. #9: ![]() Title: X-Ray Structural Study of Leghemoglobin. III. Crystallographic Data Regarding the Structure of the First Component Authors: Arutyunyan, E.G. / Kuranova, I.P. / Grebenko, A.I. / Voronova, A.A. #10: ![]() Title: The Haem-Accessibility in Leghaemoglobin of Lupinus Luteus as Observed by Proton Magnetic Relaxation Authors: Vuk-Pavlovic, S. / Benko, B. / Maricic, S. / Lahajnar, G. / Kuranova, I.P. / Vainshtein, B.K. #11: ![]() Title: X-Ray Study of Leghemoglobin. II. Determination of the Structure with Resolution of 5 Angstroms Authors: Vainshtein, B.K. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Konareva, N.V. #12: ![]() Title: X-Ray Study of Leghemoglobin. I. Purification, Crystallization, and Preparation of Derivatives Containing Heavy Atoms Authors: Vainshtein, B.K. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Konareva, N.V. #13: ![]() Title: Structure of Leghaemoglobin from Lupin Root Nodules at 5 Angstroms Resolution Authors: Vainshtein, B.K. / Harutyunyan, E.H. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovsky, A.G. / Grebenko, A.I. / Konareva, N.V. #14: ![]() Title: The X-Ray Structural Study of Leghemoglobin. II. Determination of the Structure at 5 Angstroms Resolution (Russian) Authors: Vainshtein, B.K. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Konareva, N.V. #15: ![]() Title: The X-Ray Structural Study of Leghemoglobin. I. Purification, Crystallization, and Production of Derivatives Containing Heavy Atoms (Russian) Authors: Vainshtein, B.K. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Konareva, N.V. #16: ![]() Title: X-Ray Determination of Three-Dimensional Structure of Leghemoglobin from Lupinus Luteus L. At 5 Angstroms Resolution (Russian) Authors: Vainshtein, B.K. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Konareva, N.V. #17: ![]() Title: X-Ray Diffraction Determination of the Three-Dimensional Structure of Leghemoglobin of Lupinus Luteus L. With 5 Angstroms Resolution Authors: Vainshtein, B.K. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Konareva, N.V. #18: ![]() Title: Cell Parameters of Crystalline Plant (Lupinus Luteus (Lupine)) Hemoglobin (Russian) Authors: Arutyunyan, E.G. / Zaitsev, V.N. / Zhiznevskaya, G.Ya. / Borodenko, L.I. #19: ![]() Title: Unit-Cell Parameters of Crystalline Plant Hemoglobin Authors: Arutyunyan, E.G. / Zaitsev, V.N. / Zhiznevskaya, G.Ya. / Borodenko, L.I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.9 KB | Display | ![]() |
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PDB format | ![]() | 34.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.7 KB | Display | ![]() |
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Full document | ![]() | 480.6 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16674.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-OXY / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.22 % |
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Crystal grow | *PLUS Method: other / Details: none |
-Data collection
Reflection | Resolution: 1.7→7.7 Å / Num. obs: 13765 / % possible obs: 68.7 % / Observed criterion σ(I): 1 |
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Reflection | *PLUS % possible obs: 84 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.05 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→7.7 Å / σ(F): 1 Details: THE FIRST AND LAST RESIDUES OF THE PROTEIN CHAIN ARE POORLY REVEALED IN THE ELECTRON DENSITY SYNTHESIS.
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Refinement step | Cycle: LAST / Resolution: 1.7→7.7 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.8 Å2 |