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- PDB-2gdm: LEGHEMOGLOBIN (OXY) -

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Basic information

Entry
Database: PDB / ID: 2gdm
TitleLEGHEMOGLOBIN (OXY)
ComponentsLEGHEMOGLOBIN (OXY)
KeywordsOXYGEN TRANSPORT / LEGHEMOGLOBIN / LUPINE
Function / homology
Function and homology information


nodulation / response to nitrate / nitrogen fixation / oxygen carrier activity / oxygen binding / heme binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Leghemoglobin-2
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsHarutyunyan, 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.
Citation
#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.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.
#8: 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.
#9: 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.
#10: 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.
#11: 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.
#12: 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.
#13: 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.
#14: 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.
#15: 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.
#16: 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. / Arutyunyan, E.G. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovskii, A.G. / Grebenko, A.I. / Konareva, N.V.
#17: 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.
#18: 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.
#19: 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
DepositionSep 14, 1994Processing site: BNL
SupersessionOct 15, 1995ID: 1GDM
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 29, 2014Group: Derived calculations
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEGHEMOGLOBIN (OXY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3233
Polymers16,6741
Non-polymers6482
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.190, 51.950, 38.300
Angle α, β, γ (deg.)90.00, 98.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LEGHEMOGLOBIN (OXY)


Mass: 16674.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lupinus luteus (yellow lupine) / Tissue: ROOT NODULES / References: UniProt: P02240
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal grow
*PLUS
Method: other / Details: none

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Data collection

ReflectionResolution: 1.7→7.7 Å / Num. obs: 13765 / % possible obs: 68.7 % / Observed criterion σ(I): 1
Reflection
*PLUS
% possible obs: 84 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.05

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 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.
RfactorNum. reflection% reflection
obs0.158 13765 68.7 %
Refinement stepCycle: LAST / Resolution: 1.7→7.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 45 156 1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.02
X-RAY DIFFRACTIONp_angle_d0.0430.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0230.02
X-RAY DIFFRACTIONp_chiral_restr0.0540.06
X-RAY DIFFRACTIONp_singtor_nbd0.20.3
X-RAY DIFFRACTIONp_multtor_nbd0.30.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.30.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.415
X-RAY DIFFRACTIONp_staggered_tor2020
X-RAY DIFFRACTIONp_orthonormal_tor27.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.8 Å2

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