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- PDB-1ebc: SPERM WHALE MET-MYOGLOBIN:CYANIDE COMPLEX -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1ebc
TitleSPERM WHALE MET-MYOGLOBIN:CYANIDE COMPLEX
ComponentsPROTEIN (MYOGLOBIN)
KeywordsHEMOPROTEIN / OXIGEN STORAGE / GLOBINS
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å
AuthorsRosano, C. / Ascenzi, P. / Rizzi, M. / Losso, R. / Bolognesi, M.
CitationJournal: Biophys.J. / Year: 1999
Title: Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study.
Authors: Bolognesi, M. / Rosano, C. / Losso, R. / Borassi, A. / Rizzi, M. / Wittenberg, J.B. / Boffi, A. / Ascenzi, P.
History
DepositionMar 4, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9744
Polymers17,2351
Non-polymers7393
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.870, 31.000, 35.290
Angle α, β, γ (deg.)90.00, 105.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (MYOGLOBIN)


Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.5 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.8 / Method: vapor diffusion / Details: Rizzi, M., (1994) J. Mol. Biol., 244, 86.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.05 Macetate1drop
31.3 Mammonium sulfate1drop
42.6 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→15.34 Å / Num. obs: 14099 / % possible obs: 97 % / Redundancy: 2.4 %
Reflection
*PLUS
Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
TNT5Erefinement
MOSFLMdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 1.8→15.3 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
Num. reflection% reflection
all14099 -
obs14099 97 %
Solvent computationBsol: 150 Å2 / ksol: 0.89 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→15.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 50 66 1332
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01413030.3
X-RAY DIFFRACTIONt_angle_deg2.7517470.25
X-RAY DIFFRACTIONt_dihedral_angle_d15.3737580
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011290.55
X-RAY DIFFRACTIONt_gen_planes0.0191830.82
X-RAY DIFFRACTIONt_it3.37612440.59
X-RAY DIFFRACTIONt_nbd0.024152.7
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d0.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg015.373
X-RAY DIFFRACTIONt_planar_d0.550.011
X-RAY DIFFRACTIONt_plane_restr0.820.019

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