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- PDB-8vj5: Peroxide-Soaked MnSOD -

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Basic information

Entry
Database: PDB / ID: 8vj5
TitlePeroxide-Soaked 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 / response to isolation stress / superoxide dismutase / 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
: / HYDROGEN PEROXIDE / PHOSPHATE ION / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 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)45,0968
Polymers44,7292
Non-polymers3686
Water11,061614
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)90,19316
Polymers89,4574
Non-polymers73612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area9390 Å2
ΔGint-62 kcal/mol
Surface area32350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.348, 78.348, 236.628
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-384-

HOH

21A-526-

HOH

31B-360-

HOH

41B-591-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 44 or resid 46 through 198 or resid 201 through 207))
d_2ens_1(chain "B" and (resid 0 through 44 or resid 46 through 198 or resid 201 through 207))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETLYSLYSAA0 - 441 - 45
d_12GLNGLNLYSLYSAA46 - 19847 - 199
d_13MNMNMNMNAC201
d_14PEOPEOPEOPEOAD202
d_21METMETLYSLYSBB0 - 441 - 45
d_22GLNGLNLYSLYSBB46 - 19847 - 199
d_23MNMNMNMNBF201
d_24PEOPEOPEOPEOBG202

NCS oper: (Code: givenMatrix: (-0.992022273213, 0.014091355115, -0.125272675237), (0.0113900143039, -0.979649433807, -0.200392750407), (-0.125547110776, -0.200220929357, 0.97167355754)Vector: 72. ...NCS oper: (Code: given
Matrix: (-0.992022273213, 0.014091355115, -0.125272675237), (0.0113900143039, -0.979649433807, -0.200392750407), (-0.125547110776, -0.200220929357, 0.97167355754)
Vector: 72.028458847, 74.4016761788, 12.3695986052)

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Components

#1: Protein Superoxide dismutase [Mn], mitochondrial


Mass: 22364.307 Da / Num. of mol.: 2
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.8 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 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 38708 / % possible obs: 88.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 19.24 Å2 / CC1/2: 0.872 / Rpim(I) all: 0.104 / Net I/σ(I): 5.96
Reflection shellResolution: 1.76→1.8 Å / Num. unique obs: 2947 / CC1/2: 0.732 / Rpim(I) all: 0.278

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→34.1 Å / SU ML: 0.1796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2023
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2177 1800 5 %
Rwork0.1975 34209 -
obs0.1985 35998 82.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.76→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 16 614 3792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313278
X-RAY DIFFRACTIONf_angle_d0.57164451
X-RAY DIFFRACTIONf_chiral_restr0.0414455
X-RAY DIFFRACTIONf_plane_restr0.0038579
X-RAY DIFFRACTIONf_dihedral_angle_d11.08251177
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.648498015703 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.34091110.27262113X-RAY DIFFRACTION67.52
1.81-1.860.23881190.23142265X-RAY DIFFRACTION72.57
1.86-1.920.24261240.21572344X-RAY DIFFRACTION75.27
1.92-1.990.28181270.21652411X-RAY DIFFRACTION77.4
1.99-2.070.26561290.21192459X-RAY DIFFRACTION78.07
2.07-2.160.23141310.19822497X-RAY DIFFRACTION79.71
2.16-2.280.21961360.19242573X-RAY DIFFRACTION81.55
2.28-2.420.24481400.19142662X-RAY DIFFRACTION84.07
2.42-2.610.22071450.20492773X-RAY DIFFRACTION86.97
2.61-2.870.24871530.21192882X-RAY DIFFRACTION90.54
2.87-3.280.22911580.20032996X-RAY DIFFRACTION92.28
3.28-4.130.16721580.17173004X-RAY DIFFRACTION91.39
4.14-34.10.18921690.19143230X-RAY DIFFRACTION92.09

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