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- PDB-8vhy: Neutron Structure of Reduced Trp161Phe MnSOD -

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Basic information

Entry
Database: PDB / ID: 8vhy
TitleNeutron Structure of Reduced Trp161Phe 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 / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress ...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 / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / positive regulation of vascular associated smooth muscle cell apoptotic process / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / negative regulation of vascular associated smooth muscle cell proliferation / superoxide anion generation / cellular response to ethanol / hydrogen peroxide biosynthetic process / response to manganese ion / intrinsic apoptotic signaling pathway in response to oxidative stress / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / response to zinc ion / negative regulation of fat cell differentiation / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / hemopoiesis / response to immobilization stress / response to axon injury / response to hyperoxia / neuron development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to electrical stimulus / negative regulation of fibroblast proliferation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / respiratory electron transport chain / removal of superoxide radicals / release of cytochrome c from mitochondria / post-embryonic development / liver development / regulation of mitochondrial membrane potential / response to activity / locomotory behavior / response to gamma radiation / regulation of blood pressure / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / multicellular organismal-level iron ion homeostasis / oxygen binding / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / heart development / manganese ion binding / cellular response to oxidative stress / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / 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 / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / 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. / Lutz, W.E. / 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: Biorxiv / Year: 2024
Title: Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition.
Authors: Azadmanesh, J. / Slobodnik, K. / Struble, L.R. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Myles, D.A.A. / Kroll, T. / Borgstahl, G.E.O.
History
DepositionJan 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: 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)44,7604
Polymers44,6512
Non-polymers1102
Water8,395466
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-2 kcal/mol
Surface area18080 Å2
Unit cell
Length a, b, c (Å)78.110, 78.110, 236.320
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: 22325.271 Da / Num. of mol.: 2 / Mutation: W161F
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.: 466 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 296 K / Method: vapor diffusion, sitting drop / Details: 1.93 M Potassium Phosphate

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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 22, 2022
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.3→14.74 Å / Num. obs: 18253 / % possible obs: 92.6 % / Redundancy: 4.2 % / Biso Wilson estimate: -1.09 Å2 / CC1/2: 0.84 / Rpim(I) all: 0.122 / Net I/σ(I): 4.8
Reflection shellResolution: 2.3→2.42 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1632 / CC1/2: 0.407

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→14.74 Å / SU ML: 0.334 / Cross valid method: FREE R-VALUE / σ(F): 1.67 / Phase error: 24.0492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3049 911 5 %
Rwork0.2761 17304 -
obs0.2776 18215 92.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.00223246
NEUTRON DIFFRACTIONf_angle_d0.52954404
NEUTRON DIFFRACTIONf_chiral_restr0.0378454
NEUTRON DIFFRACTIONf_plane_restr0.0038631
NEUTRON DIFFRACTIONf_dihedral_angle_d11.79711172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.30351180.29562251NEUTRON DIFFRACTION86.52
2.42-2.570.31331240.29282348NEUTRON DIFFRACTION89.92
2.57-2.770.35711290.29972451NEUTRON DIFFRACTION93.11
2.77-3.050.32071320.28622521NEUTRON DIFFRACTION95.29
3.05-3.480.29061370.2722589NEUTRON DIFFRACTION96.87
3.48-4.370.27281350.23932568NEUTRON DIFFRACTION94.02
4.37-14.740.29351360.26662576NEUTRON DIFFRACTION89.27

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