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- PDB-8kfi: Crystal structure of sperm whale myoglobin (F43A/H64I mutant) rec... -

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Basic information

Entry
Database: PDB / ID: 8kfi
TitleCrystal structure of sperm whale myoglobin (F43A/H64I 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: 2.37 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)40,96716
Polymers38,5752
Non-polymers2,39214
Water2,054114
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4838
Polymers19,2871
Non-polymers1,1967
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4838
Polymers19,2871
Non-polymers1,1967
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.692, 79.160, 104.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: -5 - 153 / Label seq-ID: 12 - 170

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Myoglobin


Mass: 19287.312 Da / Num. of mol.: 2 / Mutation: F43A,H64I, D123N
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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.0 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: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 19766 / % possible obs: 99.9 % / Redundancy: 6.56 % / CC1/2: 0.998 / Rsym value: 0.121 / Net I/σ(I): 9.8
Reflection shellResolution: 2.37→2.46 Å / Num. unique obs: 19766 / CC1/2: 0.534 / Rsym value: 1.644

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Cootmodel building
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→43.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 21.995 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1038 5.3 %RANDOM
Rwork0.198 ---
obs0.201 18681 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---1.68 Å20 Å2
3---2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.37→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 146 114 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122754
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.171.6833740
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3223.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.05515504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.408158
X-RAY DIFFRACTIONr_chiral_restr0.1370.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022016
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.2374.3631276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.2186.5271593
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0425.1711478
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.06282.06111878
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5129 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.37→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 73 -
Rwork0.333 1366 -
obs--99.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.06090.04790.1481.5536-0.65811.60990.0506-0.05550.10660.1495-0.08430.0926-0.0195-0.01450.03370.1334-0.0039-0.01490.01340.0160.2339-4.338-15.360326.6194
21.0308-0.1261-0.38591.0299-0.03350.75810.0023-0.06750.0009-0.169-0.0544-0.1612-0.02480.11350.05220.13670.0066-0.00770.01990.02180.24829.8578-6.11479.6306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 153
2X-RAY DIFFRACTION2B-5 - 153

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