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- PDB-9bwr: X-ray Counterpart to the Neutron Structure of Reduced Tyr34Phe MnSOD -

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Basic information

Entry
Database: PDB / ID: 9bwr
TitleX-ray Counterpart to the Neutron Structure of Reduced 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 / positive regulation of vascular associated smooth muscle cell apoptotic process / response to zinc ion / superoxide metabolic process / response to isolation stress / 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 / response to immobilization stress / negative regulation of vascular associated smooth muscle cell proliferation / cellular response to ethanol / hemopoiesis / 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 / regulation of mitochondrial membrane potential / 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 / post-embryonic development / respiratory electron transport chain / response to gamma radiation / locomotory behavior / response to hydrogen peroxide / liver development / Transcriptional activation of mitochondrial biogenesis / 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 / 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
: / : / PHOSPHATE ION / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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)45,0367
Polymers44,6972
Non-polymers3395
Water14,088782
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)90,07114
Polymers89,3934
Non-polymers67810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area9950 Å2
ΔGint-70 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.086, 78.086, 235.188
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-358-

HOH

21A-467-

HOH

31A-549-

HOH

41A-680-

HOH

51A-689-

HOH

61B-331-

HOH

71B-656-

HOH

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: (-0.992485611505, 0.0166901147412, -0.121217783451), (0.00787471143769, -0.979887958585, -0.199393022796), (-0.122107738799, -0.198849261225, 0.972393269946)Vector: 71. ...NCS oper: (Code: given
Matrix: (-0.992485611505, 0.0166901147412, -0.121217783451), (0.00787471143769, -0.979887958585, -0.199393022796), (-0.122107738799, -0.198849261225, 0.972393269946)
Vector: 71.566388265, 74.0237382294, 12.0750291942)

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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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 782 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.88 %
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: May 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 65175 / % possible obs: 94.4 % / Redundancy: 8.1 % / Biso Wilson estimate: 12.25 Å2 / CC1/2: 0.847 / Rpim(I) all: 0.089 / Net I/σ(I): 7.5
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2426 / CC1/2: 0.578 / Rpim(I) all: 0.411

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→31.05 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0945
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2101 3751 3.52 %
Rwork0.1885 102728 -
obs0.1893 56759 82.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.38 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 13 782 3955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333260
X-RAY DIFFRACTIONf_angle_d0.63854426
X-RAY DIFFRACTIONf_chiral_restr0.0671454
X-RAY DIFFRACTIONf_plane_restr0.0046576
X-RAY DIFFRACTIONf_dihedral_angle_d11.8971170
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.624631064064 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.2847440.30481256X-RAY DIFFRACTION27.47
1.52-1.540.322670.25651819X-RAY DIFFRACTION39.66
1.54-1.560.2955790.25992135X-RAY DIFFRACTION46.6
1.56-1.580.2573880.25142427X-RAY DIFFRACTION53.17
1.58-1.610.2577990.23972705X-RAY DIFFRACTION58.69
1.61-1.630.25751110.23823034X-RAY DIFFRACTION65.74
1.63-1.660.29411190.24223288X-RAY DIFFRACTION72.04
1.66-1.690.25941330.23573565X-RAY DIFFRACTION77.92
1.69-1.720.24361390.23413761X-RAY DIFFRACTION82.07
1.72-1.750.29341380.23043938X-RAY DIFFRACTION85.7
1.75-1.790.25711550.2234087X-RAY DIFFRACTION89.14
1.79-1.820.24191550.22244212X-RAY DIFFRACTION91.57
1.82-1.870.24271560.21664251X-RAY DIFFRACTION92.76
1.87-1.910.24941560.20714323X-RAY DIFFRACTION93.98
1.91-1.970.22241610.21474354X-RAY DIFFRACTION94.89
1.97-2.020.20561550.19334392X-RAY DIFFRACTION95.63
2.02-2.090.24321620.18514431X-RAY DIFFRACTION96.27
2.09-2.160.21781620.17564452X-RAY DIFFRACTION97.44
2.16-2.250.21011590.17434495X-RAY DIFFRACTION97.63
2.25-2.350.19061630.17144522X-RAY DIFFRACTION98.12
2.35-2.480.20381690.17714508X-RAY DIFFRACTION98.69
2.48-2.630.17651660.18034560X-RAY DIFFRACTION99.08
2.63-2.830.19341650.18844518X-RAY DIFFRACTION98.67
2.83-3.120.20441680.18314544X-RAY DIFFRACTION98.7
3.12-3.570.1831570.16064455X-RAY DIFFRACTION96.59
3.57-4.50.17141610.15374298X-RAY DIFFRACTION94.01
4.5-31.050.18511640.18514398X-RAY DIFFRACTION95.7
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.92396035861-0.0753683326290.1006378225790.8186242221170.2210516768410.640179635676-0.00252648885708-0.00610535732728-0.02264241549860.00826489947977-0.01249412977840.0243261809844-0.05124430824130.006364022801260.001516779633970.0454677126707-0.009538887093290.0002300099787720.06180416641580.007679060780430.03109594097649.861765996531.691412058891.2462999222
20.715265774128-0.0828758067447-0.02078433564190.438562991904-0.2572838500790.369815110104-0.0002284871884730.0435634489081-0.0760322077390.02025931015690.0165835027681-0.03578365903110.05245803160220.00981793588407-0.01758324200760.06776909483750.00874493978095-0.03086858611250.114580259594-0.05623204343910.092795173546311.548117182125.170560707988.4108314109
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 0 - 198 / Label seq-ID: 1 - 199

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 0 through 198)AA
22(chain 'B' and resid 0 through 198)BC

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