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- PDB-3k91: Polysulfane Bridge in Cu-Zn Superoxide Dismutase -

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Basic information

Entry
Database: PDB / ID: 3k91
TitlePolysulfane Bridge in Cu-Zn Superoxide Dismutase
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / human cu-zn superoxide dismutase / amyotrophic lateral sclerosis / antioxidant / sulfur / polysulfane / Disease mutation / Disulfide bond / Metal-binding / Neurodegeneration / Phosphoprotein
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / cellular response to cadmium ion / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / response to amphetamine / thymus development / positive regulation of cytokine production / placenta development / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PENTASULFIDE-SULFUR / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYou, Z. / Cao, X. / Taylor, A.B. / Hart, P.J. / Levine, R.L.
CitationJournal: Biochemistry / Year: 2010
Title: Characterization of a covalent polysulfane bridge in copper-zinc superoxide dismutase .
Authors: You, Z. / Cao, X. / Taylor, A.B. / Hart, P.J. / Levine, R.L.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8343
Polymers31,6732
Non-polymers1601
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-23 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.049, 57.925, 104.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15836.590 Da / Num. of mol.: 2 / Mutation: H46R, H48Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351 / Production host: Saccharomyces Cerevisiae (brewer's yeast) / Strain (production host): EG118 / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-PS5 / PENTASULFIDE-SULFUR


Mass: 160.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: S5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 36.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17 M ammonium sulfate, 0.085 M sodium acetate, 25.5% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 20, 2007 / Details: mirrors
RadiationMonochromator: confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→27.92 Å / Num. obs: 24379 / % possible obs: 95.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 15.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 2384 / Rsym value: 0.351 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZU

1ozu


Resolution: 1.75→27.92 Å / SU ML: 0.16 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1248 5.13 %random
Rwork0.1876 ---
obs0.1892 24337 95.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.892 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.5794 Å20 Å20 Å2
2--12.2064 Å20 Å2
3----7.7542 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 5 255 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012054
X-RAY DIFFRACTIONf_angle_d0.9252771
X-RAY DIFFRACTIONf_dihedral_angle_d15.023738
X-RAY DIFFRACTIONf_chiral_restr0.058315
X-RAY DIFFRACTIONf_plane_restr0.003369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.81860.2811310.25062462X-RAY DIFFRACTION93
1.8186-1.90140.29071460.21282516X-RAY DIFFRACTION96
1.9014-2.00160.20221410.19772540X-RAY DIFFRACTION96
2.0016-2.1270.23271340.16472542X-RAY DIFFRACTION97
2.127-2.29110.22791310.17972562X-RAY DIFFRACTION96
2.2911-2.52150.25561400.19232583X-RAY DIFFRACTION96
2.5215-2.88610.21651390.19772566X-RAY DIFFRACTION96
2.8861-3.63490.21681430.17282619X-RAY DIFFRACTION96
3.6349-27.920.17711430.17612699X-RAY DIFFRACTION95

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