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- PDB-8yd3: Crystal structure of human Cu-Zn Superoxide Dismutase 1 in comple... -

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Basic information

Entry
Database: PDB / ID: 8yd3
TitleCrystal structure of human Cu-Zn Superoxide Dismutase 1 in complex with 1,2,10-Decanetriol
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / Superoxide Dismutase / ALS / oxidation / oxidoreductase-inhibitor complex / electrostatic loop
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / 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 / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
: / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsAouti, S. / Padmanabhan, B.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical Research India
CitationJournal: To Be Published
Title: Crystal structure of human Cu-Zn Superoxide Dismutase 1 in complex with 1,2,10-Decanetriol
Authors: Aouti, S. / Padmanabhan, B.
History
DepositionFeb 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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 [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,34933
Polymers159,58810
Non-polymers2,76223
Water17,421967
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8039
Polymers31,9182
Non-polymers8867
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-15 kcal/mol
Surface area13870 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4237
Polymers31,9182
Non-polymers5055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-16 kcal/mol
Surface area13740 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3316
Polymers31,9182
Non-polymers4134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-14 kcal/mol
Surface area13910 Å2
MethodPISA
4
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1734
Polymers31,9182
Non-polymers2562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-13 kcal/mol
Surface area13130 Å2
MethodPISA
5
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6197
Polymers31,9182
Non-polymers7025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-12 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.666, 202.311, 143.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 15958.757 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-A1LYN / (2S)-decane-1,2,10-triol


Mass: 190.280 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.3 M Sodium citrate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.96→82.711 Å / Num. obs: 153700 / % possible obs: 91.2 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.036 / Rrim(I) all: 0.075 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.96-1.9994.40.5932.583690.7830.3170.67599.5
5.333-82.7114.20.0338.986250.9990.0160.03498.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCv1.1.7data reduction
autoPROCv1.1.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→82.71 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 7676 5 %
Rwork0.1792 --
obs0.1807 153622 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→82.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10959 0 156 967 12082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.942
X-RAY DIFFRACTIONf_dihedral_angle_d10.0061687
X-RAY DIFFRACTIONf_chiral_restr0.0641694
X-RAY DIFFRACTIONf_plane_restr0.0062058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.30912960.26025210X-RAY DIFFRACTION99
1.99-2.010.29282770.25125309X-RAY DIFFRACTION100
2.01-2.040.30022820.24135316X-RAY DIFFRACTION100
2.04-2.050.30271120.2432374X-RAY DIFFRACTION74
2.08-2.090.2395220.224578X-RAY DIFFRACTION91
2.09-2.120.2692440.21315347X-RAY DIFFRACTION100
2.12-2.150.24012910.20725262X-RAY DIFFRACTION100
2.15-2.180.23892840.21235293X-RAY DIFFRACTION100
2.18-2.210.24352780.2145293X-RAY DIFFRACTION100
2.21-2.240.2697940.21931681X-RAY DIFFRACTION37
2.26-2.290.25991670.21523153X-RAY DIFFRACTION98
2.29-2.330.24153000.20415286X-RAY DIFFRACTION100
2.33-2.370.24562590.20865305X-RAY DIFFRACTION100
2.37-2.420.24772990.21185288X-RAY DIFFRACTION100
2.42-2.480.25742950.21085296X-RAY DIFFRACTION100
2.48-2.530.24542760.20575274X-RAY DIFFRACTION99
2.53-2.60.25412930.20645282X-RAY DIFFRACTION99
2.6-2.670.24092590.20915306X-RAY DIFFRACTION99
2.67-2.750.24822800.21235234X-RAY DIFFRACTION99
2.75-2.830.25512700.21265309X-RAY DIFFRACTION99
2.83-2.940.25892660.21845338X-RAY DIFFRACTION100
2.94-3.050.22372710.19125333X-RAY DIFFRACTION100
3.05-3.190.19462850.17955324X-RAY DIFFRACTION100
3.19-3.360.21962590.17115363X-RAY DIFFRACTION100
3.36-3.570.20162800.17045323X-RAY DIFFRACTION100
3.57-3.850.17912920.15045334X-RAY DIFFRACTION99
3.85-4.230.14292640.13185367X-RAY DIFFRACTION99
4.23-4.850.14993050.13095357X-RAY DIFFRACTION99
4.85-6.10.18182920.15165301X-RAY DIFFRACTION98
6.11-82.710.18722840.16125510X-RAY DIFFRACTION98

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