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- PDB-2qkc: Structural and Kinetic Study of the Differences between Human and... -

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Basic information

Entry
Database: PDB / ID: 2qkc
TitleStructural and Kinetic Study of the Differences between Human and E.coli Manganese Superoxide Dismutases
ComponentsSuperoxide dismutase [Mn]
KeywordsOXIDOREDUCTASE / metalloenzyme / proton wire / Acetylation / Manganese / Metal-binding / Mitochondrion / Polymorphism / Transit peptide
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 / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / cellular response to ethanol / superoxide anion generation / hydrogen peroxide biosynthetic process / response to manganese ion / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of vascular associated smooth muscle cell apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / negative regulation of fat cell differentiation / response to zinc ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / response to immobilization stress / response to axon injury / neuron development / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / response to electrical stimulus / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / glutathione metabolic process / respiratory electron transport chain / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / release of cytochrome c from mitochondria / post-embryonic development / regulation of mitochondrial membrane potential / liver development / locomotory behavior / response to activity / response to gamma radiation / Transcriptional activation of mitochondrial biogenesis / response to hydrogen peroxide / oxygen binding / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / positive regulation of nitric oxide biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to oxidative stress / heart development / manganese ion binding / 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
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZheng, J. / Domsic, J.F. / Cabelli, D. / McKenna, R. / Silverman, D.N.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and kinetic study of differences between human and Escherichia coli manganese superoxide dismutases.
Authors: Zheng, J. / Domsic, J.F. / Cabelli, D. / McKenna, R. / Silverman, D.N.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Mn]
C: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9914
Polymers43,8812
Non-polymers1102
Water2,090116
1
A: Superoxide dismutase [Mn]
C: Superoxide dismutase [Mn]
hetero molecules

A: Superoxide dismutase [Mn]
C: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9838
Polymers87,7634
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area8600 Å2
ΔGint-38 kcal/mol
Surface area31160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.108, 81.108, 242.545
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

21C-357-

HOH

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Components

#1: Protein Superoxide dismutase [Mn]


Mass: 21940.734 Da / Num. of mol.: 2 / Mutation: F66L
Source method: isolated from a genetically manipulated source
Details: expressed in E. coli SOD double knockout strain / Source: (gene. exp.) Homo sapiens (human) / Gene: SOD2 / Production host: Escherichia coli (E. coli) / Strain (production host): QC774 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.5M ammonium sulfate, 0.1M malic acid, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 10, 2007 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.1 % / Av σ(I) over netI: 38.4 / Number: 64017 / Rmerge(I) obs: 0.073 / Χ2: 4.01 / D res high: 2.3 Å / D res low: 20 Å / Num. obs: 20323 / % possible obs: 92.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.93208110.05519.7013
3.934.9390.910.0552.7862.9
3.433.9391.810.0642.9833.1
3.123.4394.410.0732.7153.3
2.93.1295.310.0822.7573.3
2.732.995.710.0912.393.3
2.592.7396.210.1022.2823.3
2.482.5996.110.1112.1613.3
2.382.4895.810.1262.153.2
2.32.3890.410.1312.0842.8
ReflectionResolution: 2.3→20 Å / Num. obs: 20323 / % possible obs: 92.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.073 / Χ2: 4.012 / Net I/σ(I): 38.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.382.80.13119302.08490.4
2.38-2.483.20.12620272.1595.8
2.48-2.593.30.11120572.16196.1
2.59-2.733.30.10220712.28296.2
2.73-2.93.30.09120772.3995.7
2.9-3.123.30.08220662.75795.3
3.12-3.433.30.07320382.71594.4
3.43-3.933.10.06420282.98391.8
3.93-4.932.90.05520492.78690.9
4.93-2030.055198019.70181

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LUV

1luv


Resolution: 2.3→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 973 4.4 %5%
Rwork0.199 ---
obs-19914 91 %-
Solvent computationBsol: 38.106 Å2
Displacement parametersBiso mean: 24.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.809 Å2-4.234 Å20 Å2
2---0.809 Å20 Å2
3---1.617 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 2 116 3220
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2311.5
X-RAY DIFFRACTIONc_scbond_it2.2292
X-RAY DIFFRACTIONc_mcangle_it1.9532
X-RAY DIFFRACTIONc_scangle_it3.42.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param

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