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- PDB-9bwm: Neutron Structure of Oxidized Tyr34Phe MnSOD -

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Basic information

Entry
Database: PDB / ID: 9bwm
TitleNeutron Structure of Oxidized Tyr34Phe MnSOD
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE / MnSOD / SOD2 / 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 / intracellular oxygen homeostasis / response to L-ascorbic acid ...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 / 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 / response to zinc ion / positive regulation of vascular associated smooth muscle cell apoptotic process / superoxide metabolic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide dismutase / response to isolation stress / negative regulation of fat cell differentiation / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / response to immobilization stress / cellular response to ethanol / hemopoiesis / negative regulation of vascular associated smooth muscle cell proliferation / mitochondrial nucleoid / response to electrical stimulus / response to hyperoxia / Mitochondrial unfolded protein response (UPRmt) / response to cadmium ion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / neuron development / response to axon injury / negative regulation of fibroblast proliferation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / release of cytochrome c from mitochondria / response to activity / response to gamma radiation / post-embryonic development / regulation of mitochondrial membrane potential / respiratory electron transport chain / locomotory behavior / response to hydrogen peroxide / liver development / Transcriptional activation of mitochondrial biogenesis / oxygen binding / multicellular organismal-level iron ion homeostasis / regulation of blood pressure / 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
: / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 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 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)44,8064
Polymers44,6972
Non-polymers1102
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-2 kcal/mol
Surface area18550 Å2
Unit cell
Length a, b, c (Å)79.285, 79.285, 240.610
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 0 - 198 / Label seq-ID: 1 - 199

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.99106201254, 0.0158568046513, -0.132456215579), (0.0152465927634, -0.97294054842, -0.230552012894), (-0.132527841257, -0.230510847872, 0.964002655756)Vector: 72. ...NCS oper: (Code: given
Matrix: (-0.99106201254, 0.0158568046513, -0.132456215579), (0.0152465927634, -0.97294054842, -0.230552012894), (-0.132527841257, -0.230510847872, 0.964002655756)
Vector: 72.8795397293, 78.578850518, 14.2227505976)

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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
Details: Crystals were grown with capillary counter-diffusion setups in microgravity. Protein was at 23 mg/ml while the precipitating agent was 4 M potassium phosphate pH 7.8

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Data collection

DiffractionMean temperature: 298 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 6, 2020
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.28→14.39 Å / Num. obs: 20703 / % possible obs: 97.78 % / Redundancy: 7.79 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.953 / Rpim(I) all: 0.09 / Net I/σ(I): 7.4
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 1819 / CC1/2: 0.476 / Rpim(I) all: 0.127

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→14.39 Å / SU ML: 0.302 / Cross valid method: FREE R-VALUE / σ(F): 2.29 / Phase error: 21.7497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 2000 9.66 %
Rwork0.2422 18703 -
obs0.2454 20703 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.00116805
NEUTRON DIFFRACTIONf_angle_d0.504912202
NEUTRON DIFFRACTIONf_chiral_restr0.0358454
NEUTRON DIFFRACTIONf_plane_restr0.0021208
NEUTRON DIFFRACTIONf_dihedral_angle_d11.55831910
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.520278119884 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.340.2891200.30641125NEUTRON DIFFRACTION84.69
2.34-2.40.36971390.31821304NEUTRON DIFFRACTION97.76
2.4-2.470.34991400.30881305NEUTRON DIFFRACTION98.03
2.47-2.550.32951400.30651305NEUTRON DIFFRACTION97.9
2.55-2.640.30081410.2961323NEUTRON DIFFRACTION98.19
2.64-2.750.33461420.27721322NEUTRON DIFFRACTION99.12
2.75-2.870.29791410.27911324NEUTRON DIFFRACTION99.46
2.87-3.020.31611430.26761341NEUTRON DIFFRACTION99.46
3.02-3.210.28471450.24881350NEUTRON DIFFRACTION99.73
3.21-3.450.28321470.22351371NEUTRON DIFFRACTION99.67
3.45-3.80.24461480.20441379NEUTRON DIFFRACTION100
3.8-4.330.21451470.17631383NEUTRON DIFFRACTION99.93
4.33-5.410.1791510.17711417NEUTRON DIFFRACTION99.68
5.41-14.390.28441560.23191454NEUTRON DIFFRACTION95.49

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