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- PDB-9bwq: X-ray Counterpart to the Neutron Structure of Peroxide-Soaked Tyr... -

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Basic information

Entry
Database: PDB / ID: 9bwq
TitleX-ray Counterpart to the Neutron Structure of Peroxide-Soaked 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 / regulation of mitochondrial membrane potential / post-embryonic development / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

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)45,1659
Polymers44,6972
Non-polymers4687
Water10,287571
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-27 kcal/mol
Surface area18710 Å2
Unit cell
Length a, b, c (Å)78.221, 78.221, 239.501
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-334-

HOH

21A-353-

HOH

31B-324-

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 202))
d_2ens_1(chain "B" and (resid 0 through 44 or resid 46 through 198 or resid 202))

NCS domain segments:

Ens-ID: ens_1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETAA0 - 441 - 45
d_12GLNGLNAA46 - 19847 - 199
d_21METMETBB0 - 441 - 45
d_22GLNGLNBB46 - 19847 - 199

NCS oper: (Code: givenMatrix: (-0.991190421017, 0.013872955909, -0.131715945803), (0.0160580160965, -0.974574657999, -0.22348685891), (-0.131467446174, -0.223633130552, 0.965766293425)Vector: 72. ...NCS oper: (Code: given
Matrix: (-0.991190421017, 0.013872955909, -0.131715945803), (0.0160580160965, -0.974574657999, -0.22348685891), (-0.131467446174, -0.223633130552, 0.965766293425)
Vector: 72.1173753396, 76.8624660502, 13.6549170528)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Superoxide dismutase [Mn], mitochondrial


Mass: 22348.307 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

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Non-polymers , 5 types, 578 molecules

#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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.8 M potassium phosphate pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→39.13 Å / Num. obs: 85139 / % possible obs: 98.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 14.85 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 7.3
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 8221 / CC1/2: 0.788 / Rpim(I) all: 0.324

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→39.11 Å / SU ML: 0.153 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.1179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2052 2000 2.35 %
Rwork0.1844 83129 -
obs0.1849 85129 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.65 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 20 571 3751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373276
X-RAY DIFFRACTIONf_angle_d0.68294449
X-RAY DIFFRACTIONf_chiral_restr0.0688455
X-RAY DIFFRACTIONf_plane_restr0.0048578
X-RAY DIFFRACTIONf_dihedral_angle_d11.61391175
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.716736371786 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.29311380.28865711X-RAY DIFFRACTION97.34
1.44-1.470.30121380.26835795X-RAY DIFFRACTION97.71
1.47-1.520.25771390.23595762X-RAY DIFFRACTION98.17
1.52-1.570.24781410.21165855X-RAY DIFFRACTION98.62
1.57-1.620.22171400.19535825X-RAY DIFFRACTION98.82
1.62-1.690.2231400.19885799X-RAY DIFFRACTION98.2
1.69-1.760.21611420.18945928X-RAY DIFFRACTION99.18
1.76-1.860.23381430.18885928X-RAY DIFFRACTION99.31
1.86-1.970.19831430.17815930X-RAY DIFFRACTION99.54
1.97-2.130.21051440.1725975X-RAY DIFFRACTION99.61
2.13-2.340.2061430.17565929X-RAY DIFFRACTION98.41
2.34-2.680.20731460.18526077X-RAY DIFFRACTION99.95
2.68-3.370.18521480.19156170X-RAY DIFFRACTION100
3.37-39.110.1811550.15936445X-RAY DIFFRACTION98.73

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