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- PDB-7dgl: The Ni-bound dimeric structure of K78H/G80A/H82A myoglobin -

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Basic information

Entry
Database: PDB / ID: 7dgl
TitleThe Ni-bound dimeric structure of K78H/G80A/H82A myoglobin
ComponentsMyoglobin
KeywordsOXYGEN BINDING / OXYGEN STORAGE
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / OXYGEN ATOM / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
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.
History
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
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)35,2618
Polymers33,8792
Non-polymers1,3826
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-111 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.819, 63.276, 83.267
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: 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) / References: UniProt: P68082
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.32 %
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

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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: 1.91→46.98 Å / Num. obs: 23917 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.9
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3452 / CC1/2: 0.705

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VM9

3vm9


Resolution: 1.91→46.93 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.855 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26226 1191 5 %RANDOM
Rwork0.20889 ---
obs0.21153 22676 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.486 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å2-0 Å2
2---1.13 Å20 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.91→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 90 133 2615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132570
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172400
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6943472
X-RAY DIFFRACTIONr_angle_other_deg1.3571.6185575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6524.505111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91315451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.605154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022858
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02518
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_it2.8163.7771227
X-RAY DIFFRACTIONr_mcbond_other2.7853.7671225
X-RAY DIFFRACTIONr_mcangle_it3.7665.6541532
X-RAY DIFFRACTIONr_mcangle_other3.7525.6551532
X-RAY DIFFRACTIONr_scbond_it3.5544.1111343
X-RAY DIFFRACTIONr_scbond_other3.544.1141335
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4365.9611940
X-RAY DIFFRACTIONr_long_range_B_refined6.81144.2073025
X-RAY DIFFRACTIONr_long_range_B_other6.79144.093003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.912→1.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 87 -
Rwork0.302 1640 -
obs--99.88 %

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