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- PDB-8vj4: X-ray Counterpart to the Neutron Structure of Peroxide-Soaked Trp... -

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Basic information

Entry
Database: PDB / ID: 8vj4
TitleX-ray Counterpart to the Neutron Structure of Peroxide-Soaked Trp161Phe 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 / 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 / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / detection of oxygen / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / intracellular oxygen homeostasis / response to superoxide / response to selenium ion / cellular response to ethanol / hydrogen peroxide biosynthetic process / response to manganese ion / 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 / negative regulation of fat cell differentiation / superoxide dismutase / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / mitochondrial nucleoid / response to immobilization stress / response to axon injury / response to hyperoxia / Mitochondrial unfolded protein response (UPRmt) / neuron development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to electrical stimulus / 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 / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / liver development / post-embryonic development / response to activity / respiratory electron transport chain / response to gamma radiation / locomotory behavior / Transcriptional activation of mitochondrial biogenesis / response to hydrogen peroxide / 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 / 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 / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsAzadmanesh, J. / Slobodnik, K. / Struble, L.R. / Lutz, W.E. / 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
Citation
Journal: Nat Commun / 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.
#1: Journal: 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 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)44,8286
Polymers44,6512
Non-polymers1784
Water8,287460
1
A: Superoxide dismutase [Mn], mitochondrial
B: Superoxide dismutase [Mn], mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)89,65712
Polymers89,3014
Non-polymers3568
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area8800 Å2
ΔGint-45 kcal/mol
Surface area31380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.656, 77.656, 234.194
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
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

21A-459-

HOH

31B-326-

HOH

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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: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.80 M Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 48362 / % possible obs: 99.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.34 Å2 / CC1/2: 0.92 / Rpim(I) all: 0.056 / Net I/σ(I): 11.41
Reflection shellResolution: 1.68→1.72 Å / Num. unique obs: 4488 / CC1/2: 0.769

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→38.83 Å / SU ML: 0.2275 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2422 3423 4.15 %
Rwork0.1953 79051 -
obs0.1972 47909 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.34 Å2
Refinement stepCycle: LAST / Resolution: 1.68→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 6 460 3622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01093262
X-RAY DIFFRACTIONf_angle_d1.05434425
X-RAY DIFFRACTIONf_chiral_restr0.0649455
X-RAY DIFFRACTIONf_plane_restr0.0074579
X-RAY DIFFRACTIONf_dihedral_angle_d13.95161177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.3575890.3152026X-RAY DIFFRACTION56.55
1.7-1.730.3687890.32012204X-RAY DIFFRACTION60.52
1.73-1.760.4044970.32022365X-RAY DIFFRACTION66.34
1.76-1.790.34661150.3172688X-RAY DIFFRACTION75.17
1.79-1.820.35931400.31993052X-RAY DIFFRACTION84.33
1.82-1.850.38171310.35853206X-RAY DIFFRACTION88.99
1.85-1.890.42271460.30713340X-RAY DIFFRACTION93.51
1.89-1.920.31721490.26373451X-RAY DIFFRACTION96.21
1.92-1.970.29031520.23363406X-RAY DIFFRACTION95.18
1.97-2.010.23291470.19413491X-RAY DIFFRACTION97.12
2.01-2.060.26061500.17913545X-RAY DIFFRACTION98.48
2.06-2.120.23811560.17513559X-RAY DIFFRACTION98.86
2.12-2.180.21271530.17683540X-RAY DIFFRACTION99.11
2.18-2.250.22241540.17643538X-RAY DIFFRACTION99.03
2.25-2.330.21911560.1753596X-RAY DIFFRACTION99.26
2.33-2.420.24161510.17283589X-RAY DIFFRACTION99.6
2.42-2.530.22161530.18193568X-RAY DIFFRACTION99.63
2.53-2.670.28251610.20173587X-RAY DIFFRACTION99.6
2.67-2.830.23851570.20383558X-RAY DIFFRACTION99.89
2.83-3.050.30481590.21273587X-RAY DIFFRACTION99.87
3.05-3.360.20251620.18783571X-RAY DIFFRACTION99.28
3.36-3.850.21461470.15963537X-RAY DIFFRACTION97.87
3.85-4.840.18041550.14023500X-RAY DIFFRACTION97.62
4.85-38.830.18821540.17983547X-RAY DIFFRACTION98.85

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