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- PDB-6z4i: A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone d... -

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Basic information

Entry
Database: PDB / ID: 6z4i
TitleA4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 3 in P21 space group
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1 / ebselen / Motor neuron disease
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / myeloid cell homeostasis / regulation of GTPase activity / 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 / neuronal action potential / response to axon injury / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / peroxisome / Platelet degranulation / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / intracellular iron ion homeostasis / response to ethanol / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / 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 (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-Q85 / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAmporndanai, K. / Hasnain, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateWA1128 United States
CitationJournal: Ebiomedicine / Year: 2020
Title: Novel Selenium-based compounds with therapeutic potential for SOD1-linked amyotrophic lateral sclerosis.
Authors: Amporndanai, K. / Rogers, M. / Watanabe, S. / Yamanaka, K. / O'Neill, P.M. / Hasnain, S.S.
History
DepositionMay 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Superoxide dismutase [Cu-Zn]
FFF: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,24413
Polymers31,7112
Non-polymers1,53311
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-117 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.334, 68.260, 50.706
Angle α, β, γ (deg.)90.000, 105.711, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA FFF)

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Components

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Protein , 1 types, 2 molecules AAAFFF

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


Mass: 15855.613 Da / Num. of mol.: 2 / Mutation: A4V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pET303C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 5 types, 228 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-Q85 / ~{N}-[(4-methoxyphenyl)methyl]-2-selanyl-benzamide


Mass: 320.245 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H15NO2Se / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mM NaOAc pH 4.7, 150mM NaCl, 2.7M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.85 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 12, 2019 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.6→32.483 Å / Num. obs: 33208 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.834 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.068 / Rrim(I) all: 0.098 / Net I/σ(I): 6.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2 / Num. unique obs: 1616 / CC1/2: 0.774 / Rpim(I) all: 0.364 / Rrim(I) all: 0.541 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UXM

1uxm


Resolution: 1.6→32.46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.038 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2171 1632 4.918 %
Rwork0.1858 31551 -
all0.187 --
obs-33183 99.937 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0.692 Å2
2---0.55 Å20 Å2
3---0.068 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 79 217 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132413
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172165
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6313265
X-RAY DIFFRACTIONr_angle_other_deg1.4661.5885050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.0035.168328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38524.182110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97815380
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg26.966153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.473158
X-RAY DIFFRACTIONr_chiral_restr0.080.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022999
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02461
X-RAY DIFFRACTIONr_nbd_refined0.2890.2650
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22012
X-RAY DIFFRACTIONr_nbtor_refined0.1550.21103
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.237
X-RAY DIFFRACTIONr_metal_ion_refined0.2010.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4010.253
X-RAY DIFFRACTIONr_nbd_other0.220.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.26
X-RAY DIFFRACTIONr_mcbond_it2.3242.421263
X-RAY DIFFRACTIONr_mcbond_other2.2992.4191260
X-RAY DIFFRACTIONr_mcangle_it3.1983.6341582
X-RAY DIFFRACTIONr_mcangle_other3.1983.6341583
X-RAY DIFFRACTIONr_scbond_it2.7272.6981150
X-RAY DIFFRACTIONr_scbond_other2.7262.6981151
X-RAY DIFFRACTIONr_scangle_it4.0523.9391679
X-RAY DIFFRACTIONr_scangle_other4.0513.941680
X-RAY DIFFRACTIONr_lrange_it5.29546.4179994
X-RAY DIFFRACTIONr_lrange_other5.29546.4159995
X-RAY DIFFRACTIONr_ncsr_local_group_10.1210.054507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.2621230.2462281X-RAY DIFFRACTION99.8339
1.642-1.6860.2441110.2422266X-RAY DIFFRACTION100
1.686-1.7350.2541170.2142226X-RAY DIFFRACTION99.9573
1.735-1.7890.2441170.2122115X-RAY DIFFRACTION99.8658
1.789-1.8470.233970.1832078X-RAY DIFFRACTION99.954
1.847-1.9120.2131110.1842010X-RAY DIFFRACTION100
1.912-1.9840.234860.1871948X-RAY DIFFRACTION100
1.984-2.0650.2041000.1841859X-RAY DIFFRACTION99.8471
2.065-2.1570.197890.1781786X-RAY DIFFRACTION99.9467
2.157-2.2620.2111040.171717X-RAY DIFFRACTION100
2.262-2.3840.182880.1621634X-RAY DIFFRACTION99.884
2.384-2.5280.184790.1791538X-RAY DIFFRACTION100
2.528-2.7020.193890.1861441X-RAY DIFFRACTION100
2.702-2.9180.23670.1851355X-RAY DIFFRACTION99.9297
2.918-3.1950.221590.1861259X-RAY DIFFRACTION100
3.195-3.570.26430.1871141X-RAY DIFFRACTION100
3.57-4.1190.191500.172998X-RAY DIFFRACTION100
4.119-5.0350.145340.153863X-RAY DIFFRACTION100
5.035-7.0840.236490.194654X-RAY DIFFRACTION100
7.084-32.460.387190.27382X-RAY DIFFRACTION98.7685

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