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- PDB-7dgj: The dimeric structure of K78H/G80A/H82A myoglobin -

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Basic information

Database: PDB / ID: 7dgj
TitleThe dimeric structure of K78H/G80A/H82A myoglobin
Function / homology
Function and homology information

oxygen transport / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
Similarity search - Component
Biological speciesEquus caballus (horse)
AuthorsNagao, S. / Idomoto, A. / Shibata, N. / Higuchi, Y. / Hirota, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16K17935 Japan
Japan Society for the Promotion of Science (JSPS)JP19K05695 Japan
Japan Society for the Promotion of Science (JSPS)JP26288080 Japan
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Rational design of metal-binding sites in domain-swapped myoglobin dimers.
Authors: Nagao, S. / Idomoto, A. / Shibata, N. / Higuchi, Y. / Hirota, S.
DepositionNov 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

Structure visualization

Structure viewerMolecule:

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Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules

Theoretical massNumber of molelcules
Total (without water)35,1446

  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-90 kcal/mol
Surface area14470 Å2
Unit cell
Length a, b, c (Å)57.442, 62.695, 83.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121


#1: Protein Myoglobin /

Mass: 16939.438 Da / Num. of mol.: 2 / Mutation: K78H, G80A, H82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) / References: UniProt: P68082

Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O / OXYGEN ATOM / Oxygen

Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium acetate, 0.1 M Tris-HCl, 25% (w/v) PEG 6,000

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 40403 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17
Reflection shellResolution: 1.6→1.68 Å / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5671 / CC1/2: 0.72


XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VM9
Resolution: 1.6→47.33 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.346 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24472 2052 5.1 %RANDOM
Rwork0.20722 ---
obs0.20912 38261 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.028 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å2-0 Å2
2---0.89 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.6→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 88 173 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172390
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.6953454
X-RAY DIFFRACTIONr_angle_other_deg1.51.6185552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2235304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11724.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79615450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.752154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022838
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02510
X-RAY DIFFRACTIONr_nbd_refined
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_it2.142.5491222
X-RAY DIFFRACTIONr_mcbond_other2.1332.5461220
X-RAY DIFFRACTIONr_mcangle_it2.8313.8181524
X-RAY DIFFRACTIONr_mcangle_other2.8323.8181524
X-RAY DIFFRACTIONr_scbond_it2.9972.8661324
X-RAY DIFFRACTIONr_scbond_other2.9922.8671322
X-RAY DIFFRACTIONr_scangle_other4.614.1271930
X-RAY DIFFRACTIONr_long_range_B_refined5.22730.042997
X-RAY DIFFRACTIONr_long_range_B_other5.2229.8912975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 159 -
Rwork0.283 2726 -
obs--98.46 %

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