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- PDB-8ess: Myoglobin variant Mb-cIII complex -

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Basic information

Entry
Database: PDB / ID: 8ess
TitleMyoglobin variant Mb-cIII complex
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / HEME / METALLOPROTEIN / MYOGLOBIN / DIAZOKETONE
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 domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
Chem-WRK / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBacik, J.P. / Fasan, R. / Ando, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone.
Authors: Nam, D. / Bacik, J.P. / Khade, R.L. / Aguilera, M.C. / Wei, Y. / Villada, J.D. / Neidig, M.L. / Zhang, Y. / Ando, N. / Fasan, R.
History
DepositionOct 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3906
Polymers17,2561
Non-polymers1,1345
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.701, 90.701, 45.451
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-490-

HOH

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Components

#1: Protein Myoglobin


Mass: 17256.016 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-WRK / [2,18-bis(2-carboxyethyl)-7,12-diethenyl-3,8,13,17-tetramethyl-21-(2-oxo-3-phenylpropyl)porphyrin-21-iumato(2-)-kappa~3~N~22~,N~23~,N~24~]iron(2+)


Mass: 749.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H41FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: Mb(H64G,V68A) at 2.5 mM in 20 mM Tris-HCl pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution (200 mM Tris-HCl pH 8.9 and 2.4 M ammonium sulfate) to perform hanging-drop ...Details: Mb(H64G,V68A) at 2.5 mM in 20 mM Tris-HCl pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution (200 mM Tris-HCl pH 8.9 and 2.4 M ammonium sulfate) to perform hanging-drop vapor diffusion crystallization. A crystal was transferred from the drop it was grown in to another 4 uL drop containing well solution with the addition of 10% glycerol. The drop was overlaid with 4 uL mineral oil. A micropipette tip was dipped in sodium dithionite powder and the tip was then slowly submerged into the drop to allow the dithionite crystals to be released. 1 uL of benzyl diazoketone at 500 mM (dissolved in isopropanol) was then added to the drop for a final concentration of 100 mM, then incubated for an additional 22.5 minutes. The crystal was then looped and flash-frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→39.34 Å / Num. obs: 42175 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 16.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.016 / Net I/σ(I): 27.2
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 1.742 / Mean I/σ(I) obs: 2 / Num. unique obs: 2160 / CC1/2: 0.714 / Rpim(I) all: 0.398

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M8F

6m8f


Resolution: 1.4→39.34 Å / SU ML: 0.1297 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3517 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1781 2119 5.02 %
Rwork0.1517 40053 -
obs0.1531 42172 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.52 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 73 223 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00981295
X-RAY DIFFRACTIONf_angle_d1.02181753
X-RAY DIFFRACTIONf_chiral_restr0.0715183
X-RAY DIFFRACTIONf_plane_restr0.009259
X-RAY DIFFRACTIONf_dihedral_angle_d28.0441500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.2421310.19852666X-RAY DIFFRACTION100
1.43-1.470.19641280.17472666X-RAY DIFFRACTION100
1.47-1.510.21221290.15122687X-RAY DIFFRACTION100
1.51-1.550.19731340.14782619X-RAY DIFFRACTION100
1.55-1.60.18381260.14462687X-RAY DIFFRACTION100
1.6-1.660.16881640.13372598X-RAY DIFFRACTION100
1.66-1.730.19311270.14032696X-RAY DIFFRACTION99.96
1.73-1.80.20111280.14072683X-RAY DIFFRACTION100
1.8-1.90.16431560.14062637X-RAY DIFFRACTION99.93
1.9-2.020.1611290.14712698X-RAY DIFFRACTION100
2.02-2.170.19061390.14322663X-RAY DIFFRACTION100
2.17-2.390.17711400.14082675X-RAY DIFFRACTION100
2.39-2.740.151680.15472655X-RAY DIFFRACTION100
2.74-3.450.18531840.15932642X-RAY DIFFRACTION99.82
3.45-39.340.17841360.15732781X-RAY DIFFRACTION99.97

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