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- PDB-3ed9: Carbonmonoxy Sperm Whale Myoglobin at 140 K: Laser on [30 min] -

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Basic information

Entry
Database: PDB / ID: 3ed9
TitleCarbonmonoxy Sperm Whale Myoglobin at 140 K: Laser on [30 min]
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / haem protein / myoglobin / ligand migration / photodissociation / Heme / Iron / Metal-binding / Muscle protein
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsTomita, A. / Sato, T. / Ichiyanagi, K. / Nozawa, S. / Ichikawa, H. / Chollet, M. / Kawai, F. / Park, S.-Y. / Koshihara, S. / Adachi, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin.
Authors: Tomita, A. / Sato, T. / Ichiyanagi, K. / Nozawa, S. / Ichikawa, H. / Chollet, M. / Kawai, F. / Park, S.-Y. / Tsuduki, T. / Yamato, T. / Koshihara, S. / Adachi, S.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0725
Polymers17,2351
Non-polymers8374
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.347, 30.620, 63.799
Angle α, β, γ (deg.)90.000, 105.870, 90.000
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 natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.87 Å3/Da / Density % sol: 34.31 % / Mosaicity: 0.573 °
Crystal growTemperature: 293 K / Method: batch / pH: 6
Details: 2.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW14A / Wavelength: 0.827 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2008
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 35228 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.053 / Χ2: 0.758 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.21-1.251.60.53313700.81835
1.25-1.32.10.45327030.68468.6
1.3-1.362.70.49934620.72787.9
1.36-1.433.40.41638740.75198.5
1.43-1.523.70.32139270.80799.9
1.52-1.643.70.20739670.714100
1.64-1.813.80.13239540.725100
1.81-2.073.80.07139570.772100
2.07-2.613.80.03840060.779100
2.61-503.60.02340080.78698.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MBC

1mbc


Resolution: 1.21→16.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.155 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.832 / SU B: 2.229 / SU ML: 0.044 / SU R Cruickshank DPI: 0.056 / SU Rfree: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1753 5 %RANDOM
Rwork0.167 ---
obs0.17 35204 90.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.77 Å2 / Biso mean: 16.575 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.02 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.21→16.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 55 154 1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0221304
X-RAY DIFFRACTIONr_angle_refined_deg2.9712.0641767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27424.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93315236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.784154
X-RAY DIFFRACTIONr_chiral_restr0.2310.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02958
X-RAY DIFFRACTIONr_nbd_refined0.3070.2689
X-RAY DIFFRACTIONr_nbtor_refined0.3320.2878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2113
X-RAY DIFFRACTIONr_metal_ion_refined0.5620.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.242
X-RAY DIFFRACTIONr_mcbond_it3.5471.5759
X-RAY DIFFRACTIONr_mcangle_it4.42521207
X-RAY DIFFRACTIONr_scbond_it6.4543545
X-RAY DIFFRACTIONr_scangle_it7.8824.5560
X-RAY DIFFRACTIONr_rigid_bond_restr4.08231304
X-RAY DIFFRACTIONr_sphericity_free13.4373161
X-RAY DIFFRACTIONr_sphericity_bonded7.67731270
LS refinement shellResolution: 1.212→1.243 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 54 -
Rwork0.322 992 -
all-1046 -
obs--36.54 %

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