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- PDB-1mbo: Structure and refinement of oxymyoglobin at 1.6 angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 1mbo
TitleStructure and refinement of oxymyoglobin at 1.6 angstroms resolution
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsPhillips, S.E.V.
Citation
Journal: J.Mol.Biol. / Year: 1980
Title: Structure and refinement of oxymyoglobin at 1.6 A resolution.
Authors: Phillips, S.E.
#1: Journal: Nature / Year: 1981
Title: Neutron Diffraction Reveals Oxygen-Histidine Hydrogen Bond in Oxymyoglobin
Authors: Phillips, S.E.V. / Schoenborn, B.P.
#2: Journal: Nature / Year: 1978
Title: Structure of Oxymyoglobin
Authors: Phillips, S.E.V.
#3: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1978
Title: The Structure of Oxy-Myoglobin
Authors: Phillips, S.E.V.
History
DepositionAug 27, 1981Processing site: BNL
Revision 1.0Feb 3, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 5, 2014Group: Other
Revision 2.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / 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_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / 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_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _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 / _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)17,9804
Polymers17,2351
Non-polymers7453
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.530, 31.050, 34.930
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: INSPECTION OF MAPS AT VARIOUS STAGES OF REFINEMENT INDICATED THAT SEVERAL SIDE-CHAINS AND THE C- AND N-TERMINAL RESIDUES WERE DISORDERED TO SOME DEGREE. IN MOST CASES, ONE CONFORMATION WAS VERY ...1: INSPECTION OF MAPS AT VARIOUS STAGES OF REFINEMENT INDICATED THAT SEVERAL SIDE-CHAINS AND THE C- AND N-TERMINAL RESIDUES WERE DISORDERED TO SOME DEGREE. IN MOST CASES, ONE CONFORMATION WAS VERY MUCH STRONGER THAN THE OTHER, BUT FOUR SIDE-CHAINS WERE INCLUDED IN THE MODEL WITH TWO ALTERNATE CONFORMATIONS (VAL 13, LEU 86, LEU 89, GLN 128).
2: HOH 305 IS CLOSE TO ATOM O1 OF HEM 546. SEE PAPER CITED AS JRNL REFERENCE ABOVE.

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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: Chemical ChemComp-OXY / OXYGEN MOLECULE


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


Mass: 18.015 Da / Num. of mol.: 334 / 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: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.4 / Method: unknown

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. obs: 18494 / Num. measured all: 53607 / Rmerge(I) obs: 0.065

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Processing

SoftwareName: CONSTRAINED / Version: RECIPROCAL-SPACE LEAST-SQUARES / Classification: refinement
RefinementHighest resolution: 1.6 Å
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 50 334 1601
Refinement
*PLUS
Num. reflection obs: 18494 / σ(F): 3 / Rfactor all: 0.159 / Rfactor obs: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS

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