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- PDB-8kfj: Crystal structure of sperm whale myoglobin (F46L/H64A mutant) rec... -

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Basic information

Entry
Database: PDB / ID: 8kfj
TitleCrystal structure of sperm whale myoglobin (F46L/H64A mutant) reconstituted with manganese porphycene
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / globin fold / oxygen transport / muscles
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 / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PORPHYCENE CONTAINING MN / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMizohata, E. / Oohora, K. / Hayashi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Chem Lett. / Year: 2024
Title: Rational design of an artificial ethylbenzene hydroxylase using a molecular dynamics simulation to enhance enantioselectivity.
Authors: Oohora, K. / Kagawa, Y. / Nishiura, T. / Mizohata, E. / Schwaneberg, U. / Hayashi, T.
History
DepositionAug 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Sep 3, 2025Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,09818
Polymers38,5752
Non-polymers2,52316
Water4,432246
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5199
Polymers19,2871
Non-polymers1,2318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5799
Polymers19,2871
Non-polymers1,2928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.673, 80.174, 106.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 19287.311 Da / Num. of mol.: 2 / Mutation: F46L,H64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02185
#2: Chemical ChemComp-HNN / PORPHYCENE CONTAINING MN


Mass: 619.612 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36MnN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate, 100 mM Tris-HCl buffer at pH 8.2, 4% acetone and 10% trehalose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 39037 / % possible obs: 99.9 % / Redundancy: 6.63 % / CC1/2: 0.999 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2472 / CC1/2: 0.607

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.36 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21242 1849 4.7 %RANDOM
Rwork0.17862 ---
obs0.18024 37124 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.342 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---1.62 Å20 Å2
3---2.6 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 152 246 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172613
X-RAY DIFFRACTIONr_angle_refined_deg3.9451.6893764
X-RAY DIFFRACTIONr_angle_other_deg1.5631.6196069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86423.333123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61915503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.056159
X-RAY DIFFRACTIONr_chiral_restr0.10.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022979
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02530
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2564.4261284
X-RAY DIFFRACTIONr_mcbond_other4.2244.421282
X-RAY DIFFRACTIONr_mcangle_it5.4216.6051603
X-RAY DIFFRACTIONr_mcangle_other5.3956.6061603
X-RAY DIFFRACTIONr_scbond_it5.9685.2381487
X-RAY DIFFRACTIONr_scbond_other5.6865.1251433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5797.3822080
X-RAY DIFFRACTIONr_long_range_B_refined9.99384.59111831
X-RAY DIFFRACTIONr_long_range_B_other9.98384.31411647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 155 -
Rwork0.307 2691 -
obs--99.96 %

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