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- PDB-5mbn: REFINEMENT OF MYOGLOBIN AND CYTOCHROME C -

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Basic information

Entry
Database: PDB / ID: 5mbn
TitleREFINEMENT OF MYOGLOBIN AND CYTOCHROME C
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsTakano, T.
Citation
Journal: Methods and Applications in Crystallographic Computing
Year: 1984
Title: Refinement of Myoglobin and Cytochrome C
Authors: Takano, T.
#1: Journal: J.Mol.Biol. / Year: 1977
Title: Structure of Myoglobin Refined at 2.0 Angstroms Resolution. II. Structure of Deoxymyoglobin from Sperm Whale
Authors: Takano, T.
#2: Journal: J.Mol.Biol. / Year: 1977
Title: Structure of Myoglobin Refined at 2.0 Angstroms Resolution. I. Crystallographic Refinement of Metmyoglobin from Sperm Whale
Authors: Takano, T.
#3: Journal: Prog.Stereochem. / Year: 1976
Title: The Stereochemistry of the Protein Myoglobin
Authors: Watson, H.C.
#4: Journal: Acta Crystallogr. / Year: 1966
Title: A Mathematical Model-Building Procedure for Proteins
Authors: Diamond, R.
#5: Journal: Acta Crystallogr.,Sect.A / Year: 1971
Title: A Real-Space Refinement Procedure for Proteins
Authors: Diamond, R.
#6: Journal: J.Mol.Biol. / Year: 1974
Title: Real-Space Refinement of the Structure of Hen Egg-White Lysozyme
Authors: Diamond, R.
#7: Journal: Nature / Year: 1966
Title: Structure of Deoxymyoglobin, a Crystallographic Study
Authors: Nobbs, C.L. / Watson, H.C. / Kendrew, J.C.
#8: Journal: J.Mol.Biol. / Year: 1975
Title: Three-Dimensional Fourier Synthesis of Human Deoxyhaemoglobin at 2.5 Angstroms, Refinement of the Atomic Model
Authors: Fermi, G.
#9: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionJan 14, 1988Processing site: BNL
SupersessionJul 12, 1989ID: 3MBN
Revision 1.0Jul 12, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Feb 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_database_status.process_site / _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_torsion.phi / _pdbx_validate_torsion.psi / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9483
Polymers17,2351
Non-polymers7132
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.840, 30.980, 34.920
Angle α, β, γ (deg.)90.00, 106.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOGLOBIN


Mass: 17234.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 120 / 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: 1.96 Å3/Da / Density % sol: 37.1 %

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.179 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 44 120 1381

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