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- PDB-1mbs: X-RAY CRYSTALLOGRAPHIC STUDIES OF SEAL MYOGLOBIN. THE MOLECULE AT... -

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Basic information

Entry
Database: PDB / ID: 1mbs
TitleX-RAY CRYSTALLOGRAPHIC STUDIES OF SEAL MYOGLOBIN. THE MOLECULE AT 2.5 ANGSTROMS RESOLUTION
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT
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 / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin / Myoglobin
Similarity search - Component
Biological speciesPhoca vitulina (harbor seal)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsScouloudi, H.
Citation
Journal: J.Mol.Biol. / Year: 1978
Title: X-ray crystallographic studies of seal myoglobin. The molecule at 2.5 A resolution.
Authors: Scouloudi, H. / Baker, E.N.
#1: Journal: J.Mol.Biol. / Year: 1978
Title: A Preliminary Comparison of Metmyoglobin Molecules from Seal and Sperm Whale
Authors: Scouloudi, H.
#2: Journal: J.Mol.Biol. / Year: 1977
Title: Structure of Myoglobin Refined at 2.0 Angstroms. I.Crystallographic Refinement of Metmyoglobin from Sperm Whale
Authors: Takano, T.
#3: Journal: Prog.Stereochem. / Year: 1969
Title: Stereochemistry of the Protein Myoglobin
Authors: Watson, H.C.
#4: Journal: J.Biol.Chem. / Year: 1969
Title: Comparison of Myoglobins from Harbor Seal, Porpoise and Sperm Whale. V. The Complete Amino Acid Sequences of Harbor Seal and Propoise Myoglobins
Authors: Bradshaw, R.A. / Gurd, F.R.N.
#5: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMar 22, 1979Processing site: BNL
Revision 1.0May 15, 1979Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9502
Polymers17,3341
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.810, 29.700, 106.090
Angle α, β, γ (deg.)90.00, 101.99, 90.00
Int Tables number5
Space group name H-MA121
Atom site foot note1: IN RESIDUE LYS 147 THE ORIENTATION OF THE SIDE CHAIN FROM ATOM CG IS DOUBTFUL.
2: THE ORIENTATION OF THE LAST THREE RESIDUES (PHE 151, HIS 152, GLY 153) IS UNCERTAIN.

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Components

#1: Protein MYOGLOBIN


Mass: 17333.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phoca vitulina (harbor seal) / References: UniProt: P02162, UniProt: P68080*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal grow
*PLUS
Method: other
Details: Scouloudi, H., (1960) Proc. Roy. Soc. ser. A, 258, 181., Scouloudi, H., (1969) J. Mol. Biol., 40, 353.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.5 Å
Details: AUTHORS MAINTAIN THAT THE ORIENTATION OF THE LAST THREE RESIDUES (PHE 151, HIS 152, GLY 153) IS UNCERTAIN. ALSO, IN RESIDUE LYS 147 THE ORIENTATION OF THE SIDE CHAIN FROM ATOM CG IS DOUBTFUL.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 43 0 1266

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