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- PDB-5oja: Structure of MbQ -

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Basic information

Entry
Database: PDB / ID: 5oja
TitleStructure of MbQ
ComponentsMyoglobin
KeywordsOXIDOREDUCTASE / myoglobin / NMH / N-methylhistidine / heme
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 / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.347 Å
AuthorsHayashi, T. / Pott, M. / Mori, T. / Mittl, P. / Green, A. / Hivert, D.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: A Noncanonical Proximal Heme Ligand Affords an Efficient Peroxidase in a Globin Fold.
Authors: Pott, M. / Hayashi, T. / Mori, T. / Mittl, P.R.E. / Green, A.P. / Hilvert, D.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0523
Polymers18,3661
Non-polymers6862
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-15 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.130, 51.900, 39.350
Angle α, β, γ (deg.)90.00, 98.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 18366.158 Da / Num. of mol.: 1
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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG (pH 7.0), 30% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.347→50 Å / Num. obs: 28974 / % possible obs: 96 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.77
Reflection shellResolution: 1.347→1.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 4410 / CC1/2: 0.741 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OJ9

5oj9


Resolution: 1.347→38.961 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.81
RfactorNum. reflection% reflection
Rfree0.2065 1449 5 %
Rwork0.1852 --
obs0.1863 28971 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.347→38.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 48 148 1405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061320
X-RAY DIFFRACTIONf_angle_d0.831792
X-RAY DIFFRACTIONf_dihedral_angle_d18.513479
X-RAY DIFFRACTIONf_chiral_restr0.068186
X-RAY DIFFRACTIONf_plane_restr0.004223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3467-1.39490.28871300.29952472X-RAY DIFFRACTION88
1.3949-1.45070.30671440.26642745X-RAY DIFFRACTION95
1.4507-1.51680.23111490.22022830X-RAY DIFFRACTION99
1.5168-1.59670.23821480.20212795X-RAY DIFFRACTION99
1.5967-1.69680.25741480.19482810X-RAY DIFFRACTION98
1.6968-1.82780.20051440.1972738X-RAY DIFFRACTION96
1.8278-2.01170.22041410.19592681X-RAY DIFFRACTION93
2.0117-2.30280.21831480.17562816X-RAY DIFFRACTION98
2.3028-2.90110.18921480.18972806X-RAY DIFFRACTION98
2.9011-38.97760.18991490.16742829X-RAY DIFFRACTION96

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