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- PDB-9bvy: Neutron Structure of Peroxide-Soaked Tyr34Phe MnSOD -

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Basic information

Entry
Database: PDB / ID: 9bvy
TitleNeutron Structure of Peroxide-Soaked Tyr34Phe MnSOD
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE / MnSOD / SOD2 / Product-Inhibition / PCET
Function / homology
Function and homology information


acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / detection of oxygen / response to silicon dioxide / response to isolation stress / intracellular oxygen homeostasis ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / detection of oxygen / response to silicon dioxide / response to isolation stress / intracellular oxygen homeostasis / response to L-ascorbic acid / response to selenium ion / response to superoxide / response to manganese ion / hydrogen peroxide biosynthetic process / superoxide anion generation / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of vascular associated smooth muscle cell apoptotic process / response to zinc ion / superoxide metabolic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide dismutase / negative regulation of fat cell differentiation / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / response to immobilization stress / negative regulation of vascular associated smooth muscle cell proliferation / cellular response to ethanol / hemopoiesis / mitochondrial nucleoid / response to electrical stimulus / response to hyperoxia / Mitochondrial unfolded protein response (UPRmt) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / neuron development / response to axon injury / response to cadmium ion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / liver development / release of cytochrome c from mitochondria / response to activity / respiratory electron transport chain / post-embryonic development / regulation of mitochondrial membrane potential / response to gamma radiation / locomotory behavior / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / oxygen binding / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / manganese ion binding / heart development / cellular response to oxidative stress / response to lipopolysaccharide / protein homotetramerization / negative regulation of neuron apoptotic process / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / response to xenobiotic stimulus / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding
Similarity search - Function
: / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
: / HYDROGEN PEROXIDE / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAzadmanesh, J. / Slobodnik, K. / Struble, L.R. / Cone, E.A. / Dasgupta, M. / Lutz, W.E. / Kumar, S. / Natarajan, A. / Coates, L. / Weiss, K.L. ...Azadmanesh, J. / Slobodnik, K. / Struble, L.R. / Cone, E.A. / Dasgupta, M. / Lutz, W.E. / Kumar, S. / Natarajan, A. / Coates, L. / Weiss, K.L. / Myles, D.A.A. / Kroll, T. / Borgstahl, G.E.O.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM145647 United States
National Aeronautics and Space Administration (NASA, United States)44-0307-1021-201 United States
Department of Energy (DOE, United States) United States
CitationJournal: Nat Commun / Year: 2025
Title: The role of Tyr34 in proton coupled electron transfer and product inhibition of manganese superoxide dismutase.
Authors: Azadmanesh, J. / Slobodnik, K. / Struble, L.R. / Lovelace, J.J. / Cone, E.A. / Dasgupta, M. / Lutz, W.E. / Kumar, S. / Natarajan, A. / Coates, L. / Weiss, K.L. / Myles, D.A.A. / Kroll, T. / Borgstahl, G.E.O.
History
DepositionMay 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Superoxide dismutase [Mn], mitochondrial
B: Superoxide dismutase [Mn], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8415
Polymers44,6972
Non-polymers1443
Water9,008500
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-4 kcal/mol
Surface area18630 Å2
Unit cell
Length a, b, c (Å)78.690, 78.690, 239.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Superoxide dismutase [Mn], mitochondrial


Mass: 22348.307 Da / Num. of mol.: 2 / Mutation: Y34F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04179, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: counter-diffusion / pH: 7.8
Details: Capillary counterdiffusion in microgravity. Protein was at 25 mg/ml concentration and the precipitating agent was 4 M potassium phosphate pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4
DetectorType: ORNL ANGER CAMERA / Detector: DIFFRACTOMETER / Date: Jan 20, 2022
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.3→14.84 Å / Num. obs: 18698 / % possible obs: 90.4 % / Redundancy: 4.1 % / CC1/2: 0.783 / Rpim(I) all: 0.133 / Net I/σ(I): 5.1
Reflection shellResolution: 2.3→2.37 Å / Num. unique obs: 1703 / CC1/2: 0.259 / Rpim(I) all: 0.142

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→14.84 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 1.83 / Phase error: 21.5128
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2989 933 5.01 %
Rwork0.2652 17708 -
obs0.2669 18641 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 3.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0023253
NEUTRON DIFFRACTIONf_angle_d0.54114414
NEUTRON DIFFRACTIONf_chiral_restr0.0382454
NEUTRON DIFFRACTIONf_plane_restr0.0034631
NEUTRON DIFFRACTIONf_dihedral_angle_d13.43981170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.30581210.26322313NEUTRON DIFFRACTION86.19
2.42-2.570.30851240.27072343NEUTRON DIFFRACTION87.14
2.57-2.770.35151290.27732453NEUTRON DIFFRACTION90.79
2.77-3.050.31121350.27712563NEUTRON DIFFRACTION93.62
3.05-3.480.25721380.2662630NEUTRON DIFFRACTION95.84
3.48-4.370.25671400.23972659NEUTRON DIFFRACTION94.43
4.37-14.840.31821460.27032747NEUTRON DIFFRACTION92.55

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