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- PDB-8kfh: Crystal structure of sperm whale myoglobin reconstituted with man... -

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Basic information

Entry
Database: PDB / ID: 8kfh
TitleCrystal structure of sperm whale myoglobin 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: 2.27 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,59210
Polymers38,7772
Non-polymers1,8168
Water1,74797
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3926
Polymers19,3881
Non-polymers1,0045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2004
Polymers19,3881
Non-polymers8123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.953, 80.699, 106.820
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: 19388.396 Da / Num. of mol.: 2 / Mutation: 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.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.17 Å3/Da / Density % sol: 61.14 %
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: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 23450 / % possible obs: 99.9 % / Redundancy: 6.56 % / CC1/2: 0.997 / Rsym value: 0.144 / Net I/σ(I): 9
Reflection shellResolution: 2.27→2.34 Å / Num. unique obs: 23450 / CC1/2: 0.51 / Rsym value: 1.994

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Cootmodel building
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→46.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 20.57 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1157 4.9 %RANDOM
Rwork0.203 ---
obs0.205 22241 99.9 %-
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: 51.83 Å2
Baniso -1Baniso -2Baniso -3
1-5.36 Å20 Å20 Å2
2--0.61 Å20 Å2
3----5.97 Å2
Refinement stepCycle: LAST / Resolution: 2.27→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 116 97 2769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.1611.6843777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76823.516128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.26615509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.597158
X-RAY DIFFRACTIONr_chiral_restr0.140.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022076
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_it3.6544.6531288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.146.9521609
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.755.3271494
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.82987.61311664
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.27→2.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 80 -
Rwork0.39 1608 -
obs--99.82 %
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)
11.37740.3556-0.1261.9879-0.92961.25080.1929-0.0729-0.02910.1795-0.2010.0353-0.19110.10810.00820.0516-0.03260.00170.23060.00860.5899-3.9205-16.114627.0709
21.4711-0.00740.16591.4880.07380.67860.00980.0597-0.0241-0.0769-0.0466-0.1333-0.02420.03110.03680.00520.01050.01390.21470.01620.59379.6446-6.801810.202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 153
2X-RAY DIFFRACTION2B-6 - 153

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