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- PDB-5ojc: Structure of MbQ2.1 NMH -

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Basic information

Entry
Database: PDB / ID: 5ojc
TitleStructure of MbQ2.1 NMH
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: 1.25 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)18,9253
Polymers18,2401
Non-polymers6862
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-13 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.532, 51.800, 39.660
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 18239.916 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.92 Å3/Da / Density % sol: 35.99 %
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: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→39.191 Å / Num. obs: 36215 / % possible obs: 94.9 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.4
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2 / Num. unique obs: 1764 / CC1/2: 0.811 / % possible all: 93.7

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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: 1.25→39.191 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.09
RfactorNum. reflection% reflection
Rfree0.2148 2000 5.53 %
Rwork0.1925 --
obs0.1938 36171 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→39.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 48 143 1404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061296
X-RAY DIFFRACTIONf_angle_d0.9251756
X-RAY DIFFRACTIONf_dihedral_angle_d23.606462
X-RAY DIFFRACTIONf_chiral_restr0.062182
X-RAY DIFFRACTIONf_plane_restr0.005218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.28130.31411420.30422425X-RAY DIFFRACTION94
1.2813-1.31590.29521400.25922392X-RAY DIFFRACTION94
1.3159-1.35470.29021400.23392396X-RAY DIFFRACTION94
1.3547-1.39840.28651420.22972426X-RAY DIFFRACTION94
1.3984-1.44840.25151400.21652377X-RAY DIFFRACTION92
1.4484-1.50640.20351420.19492423X-RAY DIFFRACTION95
1.5064-1.57490.23261430.18752443X-RAY DIFFRACTION95
1.5749-1.6580.22021430.19032452X-RAY DIFFRACTION95
1.658-1.76180.24531420.19552422X-RAY DIFFRACTION95
1.7618-1.89790.21991430.19412442X-RAY DIFFRACTION95
1.8979-2.08890.2041390.18772397X-RAY DIFFRACTION92
2.0889-2.39110.19461470.1832499X-RAY DIFFRACTION97
2.3911-3.01230.20781480.20132533X-RAY DIFFRACTION97
3.0123-39.210.20261490.17732544X-RAY DIFFRACTION96

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