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Yorodumi- PDB-1gdj: CRYSTAL STRUCTURE OF FERRIC COMPLEXES OF THE YELLOW LUPIN LEGHEMO... -
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Entry | Database: PDB / ID: 1gdj | |||||||||
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Title | CRYSTAL STRUCTURE OF FERRIC COMPLEXES OF THE YELLOW LUPIN LEGHEMOGLOBIN WITH ISOQUINOLINE AT 1.8 ANGSTROMS RESOLUTION (RUSSIAN) | |||||||||
Components | LEGHEMOGLOBIN (DEOXY) | |||||||||
Keywords | OXYGEN TRANSPORT | |||||||||
Function / homology | Function and homology information response to nitrate / oxygen carrier activity / oxygen binding / heme binding / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Lupinus luteus (yellow lupine) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | |||||||||
Authors | Harutyunyan, E. / Safonova, T. / Kuranova, I. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 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: Journal: Bioorg.Khim. / Year: 1991 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: Journal: Bioorg.Khim. / Year: 1988 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: Journal: Kristallografiya / Year: 1980 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: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1980 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: Journal: Kristallografiya / Year: 1978 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: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1978 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: Journal: Dokl.Akad.Nauk Sssr / Year: 1977 Title: Spatial Structure of Lupine Leghemoglobin with the 2.8 Angstroms Resolution (Russian) Authors: 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. #8: Journal: Dokl.Biochem.(Engl.Transl.) / Year: 1977 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. #9: Journal: Kristallografiya / Year: 1977 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. #10: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1977 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. #11: Journal: Int.J.Pept.Protein Res. / Year: 1976 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. #12: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1975 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. #13: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1975 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. #14: Journal: Nature / Year: 1975 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. #15: Journal: Kristallografiya / Year: 1974 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. #16: Journal: Kristallografiya / Year: 1974 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. #17: Journal: Dokl.Akad.Nauk Sssr / Year: 1974 Title: X-Ray Determination of Three-Dimensional Structure of Leghemoglobin from Lupinus Luteus L. At 5 Angstroms Resolution (Russian) Authors: Vainshtein, B.K. / Arutiunian, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Konareva, N.V. #18: Journal: Dokl.Biochem.(Engl.Transl.) / Year: 1974 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. #19: Journal: Kristallografiya / Year: 1971 Title: Cell Parameters of Crystalline Plant (Lupinus Luteus (Lupine)) Hemoglobin (Russian) Authors: Arutyunyan, E.G. / Zaitsev, V.N. / Zhiznevskaya, G.Ya. / Borodenko, L.I. #20: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1971 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: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 1gdj.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gdj.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/1gdj ftp://data.pdbj.org/pub/pdb/validation_reports/gd/1gdj | HTTPS FTP |
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-Related structure data
-Links
-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 genetically manipulated source Source: (gene. exp.) Lupinus luteus (yellow lupine) / References: UniProt: P02240 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | *PLUS Method: other / Details: none |
-Data collection
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8.3 Å / Num. obs: 14374 / % possible obs: 94 % / Observed criterion σ(F): 3 / Rmerge(I) obs: 0.05 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 1.7→8 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→8 Å
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Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.021 |