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- PDB-1mbi: X-RAY CRYSTAL STRUCTURE OF THE FERRIC SPERM WHALE MYOGLOBIN: IMID... -

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Basic information

Entry
Database: PDB / ID: 1mbi
TitleX-RAY CRYSTAL STRUCTURE OF THE FERRIC SPERM WHALE MYOGLOBIN: IMIDAZOLE COMPLEX AT 2.0 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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLionetti, C. / Guanziroli, M.G. / Frigerio, F. / Ascenzi, P. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: X-ray crystal structure of the ferric sperm whale myoglobin: imidazole complex at 2.0 A resolution.
Authors: Lionetti, C. / Guanziroli, M.G. / Frigerio, F. / Ascenzi, P. / Bolognesi, M.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.6 Angstroms Resolution
Authors: Bolognesi, M. / Onesti, S. / Gatti, G. / Coda, A. / Ascenzi, P. / Brunori, M.
#2: Journal: J.Mol.Biol. / Year: 1982
Title: Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study
Authors: Bolognesi, M. / Cannillo, E. / Ascenzi, P. / Giacometti, G.M. / Merli, A. / Brunori, M.
History
DepositionJun 25, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: 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)18,0174
Polymers17,2351
Non-polymers7823
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.900, 30.760, 34.860
Angle α, β, γ (deg.)90.00, 105.67, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: THERE ARE LIGAND INDUCED CONFORMATIONAL CHANGES IN RESIDUES HIS 64, ARG 45 AND ASP 60.

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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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal grow
*PLUS
pH: 5.75 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %protein11
2100 %ammonium sulfate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 9169 / Observed criterion σ(I): 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2→10 Å /
RfactorNum. reflection
obs0.148 8822
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 53 119 1389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.086
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection all: 8822 / Rfactor all: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS

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