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- PDB-7ylk: Myoglobin containing Ir complex -

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Basic information

Entry
Database: PDB / ID: 7ylk
TitleMyoglobin containing Ir complex
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / artificial metallocofactor
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
Chem-IRQ / Chem-KKC / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsLee, J.H. / Song, W.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Photocatalytic C-O Coupling Enzymes That Operate via Intramolecular Electron Transfer.
Authors: Lee, J. / Song, W.J.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8824
Polymers17,1061
Non-polymers1,7763
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, intact mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint4 kcal/mol
Surface area7950 Å2
Unit cell
Length a, b, c (Å)33.402, 57.882, 76.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myoglobin


Mass: 17105.807 Da / Num. of mol.: 1 / Mutation: H64A, H93A, H97A, V68A, R45C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-KKC / delta-{1-([2,2'-bipyridin]-5-ylmethyl)pyrrolidine-2,5-dione}bis[2-(2,4-difluorophenyl)pyridine)]iridium(III)


Mass: 839.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H25F4IrN5O2
#3: Chemical ChemComp-IRQ / lambda-{1-([2,2'-bipyridin]-5-ylmethyl)pyrrolidine-2,5-dione}bis[2-(2,4-difluorophenyl)pyridine)]iridium(III)


Mass: 839.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H25F4IrN5O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsIRQ and KKC are in alternate conformations of each other.

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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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.15 M (NH4)2SO4, 100 mM Tris-HCl (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.63→30.58 Å / Num. obs: 19134 / % possible obs: 99.7 % / Redundancy: 14 % / Biso Wilson estimate: 23.03 Å2 / Rsym value: 0.076 / Net I/σ(I): 63.6
Reflection shellResolution: 1.63→1.66 Å / Num. unique obs: 1768 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
MOLREPphasing
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VXA

1vxa


Resolution: 1.63→30.58 Å / SU ML: 0.1861 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 935 4.91 %
Rwork0.1916 18108 -
obs0.1936 19043 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.07 Å2
Refinement stepCycle: LAST / Resolution: 1.63→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 103 137 1447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591368
X-RAY DIFFRACTIONf_angle_d0.97241877
X-RAY DIFFRACTIONf_chiral_restr0.0441183
X-RAY DIFFRACTIONf_plane_restr0.006218
X-RAY DIFFRACTIONf_dihedral_angle_d10.1276180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.720.28741320.22722514X-RAY DIFFRACTION99.4
1.72-1.820.22851250.19842563X-RAY DIFFRACTION99.96
1.82-1.960.19571160.19832575X-RAY DIFFRACTION99.96
1.96-2.160.24311350.18312559X-RAY DIFFRACTION99.96
2.16-2.470.21791490.18922563X-RAY DIFFRACTION100
2.47-3.120.27051300.20642611X-RAY DIFFRACTION99.96
3.12-30.580.22031480.18262723X-RAY DIFFRACTION98.9

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