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- PDB-1lh3: X-RAY STRUCTURAL INVESTIGATION OF LEGHEMOGLOBIN. VI. STRUCTURE OF... -

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Entry
Database: PDB / ID: 1lh3
TitleX-RAY STRUCTURAL INVESTIGATION OF LEGHEMOGLOBIN. VI. STRUCTURE OF ACETATE-FERRILEGHEMOGLOBIN AT A RESOLUTION OF 2.0 ANGSTROMS (RUSSIAN)
ComponentsLEGHEMOGLOBIN (CYANO MET)
KeywordsOXYGEN TRANSPORT
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Leghemoglobin-2
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsVainshtein, B.K. / Harutyunyan, E.H. / Kuranova, I.P. / Borisov, V.V. / Sosfenov, N.I. / Pavlovsky, A.G. / Grebenko, A.I. / Konareva, N.V.
Citation
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.
#1: 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.
#2: 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, Y.V.
#3: 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, Y.V.
#4: 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, I.V.
#5: 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, Y.V.
#6: 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.
#7: 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.
#8: 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. / Kuranova, G. / Lahajnar, I.P. / Vainshtein, B.K.
#9: 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.
#10: 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.
#11: 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.
#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: 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.
#15: 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.
#16: Journal: Kristallografiya / Year: 1971
Title: Cell Parameters of Crystalline Plant (Lupinus Luteus (Lupine)) Hemoglobin (Russian)
Authors: Arutyunyan, E.G. / Zaitsev, V.N. / Zhiznevskaya, G.Y. / Borodenko, L.I.
#17: 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.Y. / Borodenko, L.I.
History
DepositionApr 23, 1982Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 20, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Oct 9, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation_author ...atom_site / citation_author / database_PDB_matrix / pdbx_entry_details / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_conn_angle.value / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value
Details: Coordinates transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEGHEMOGLOBIN (CYANO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3173
Polymers16,6741
Non-polymers6432
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.190, 38.410, 52.070
Angle α, β, γ (deg.)90.00, 90.00, 98.90
Int Tables number5
Space group name H-MB112
Atom site foot note1: THIS ATOM WAS NOT RESOLVED IN THE FOURIER MAP.

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Components

#1: Protein LEGHEMOGLOBIN (CYANO MET)


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
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.43 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 0 45 66 1291

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