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- PDB-6z4m: A4V mutant of human SOD1 bound with 2-(pyridin-3-ylmethyl)benzois... -

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Basic information

Entry
Database: PDB / ID: 6z4m
TitleA4V mutant of human SOD1 bound with 2-(pyridin-3-ylmethyl)benzoisoselenazolone derivative 10 in P21 space group
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1 / ebselen / Motor neuron disease
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 / glutathione metabolic process / embryo implantation / 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 / regulation of blood pressure / negative regulation of inflammatory response / 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
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
Chem-Q8E / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
Revision 1.2Nov 20, 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
AAA: Superoxide dismutase [Cu-Zn]
BBB: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,78211
Polymers31,7112
Non-polymers1,0719
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-130 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.411, 68.002, 50.903
Angle α, β, γ (deg.)90.000, 106.235, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

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Protein , 1 types, 2 molecules AAABBB

#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, 199 molecules

#2: Chemical ChemComp-Q8E / ~{N}-[(6-methoxypyridin-3-yl)methyl]-2-selanyl-benzamide


Mass: 321.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N2O2Se / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.89 %
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: I04-1 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 29, 2020 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.55→36.88 Å / Num. obs: 36425 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 16.089 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.061 / Rrim(I) all: 0.089 / Net I/σ(I): 8.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2 / Num. unique obs: 1776 / CC1/2: 0.798 / Rpim(I) all: 0.381 / Rrim(I) all: 0.571 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UXM

1uxm


Resolution: 1.55→36.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.975 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2078 1810 4.975 %
Rwork0.1949 34571 -
all0.196 --
obs-36381 99.63 %
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: 22.696 Å2
Baniso -1Baniso -2Baniso -3
1-1.203 Å20 Å2-0.068 Å2
2---0.925 Å20 Å2
3----0.204 Å2
Refinement stepCycle: LAST / Resolution: 1.55→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 49 190 2446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122384
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.6463240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0145331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69324.206107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99515378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.047159
X-RAY DIFFRACTIONr_chiral_restr0.1220.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021874
X-RAY DIFFRACTIONr_nbd_refined0.2330.21252
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.265
X-RAY DIFFRACTIONr_metal_ion_refined0.2310.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3090.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.27
X-RAY DIFFRACTIONr_mcbond_it2.3171.9821271
X-RAY DIFFRACTIONr_mcangle_it3.3092.9741602
X-RAY DIFFRACTIONr_scbond_it3.4312.3651113
X-RAY DIFFRACTIONr_scangle_it5.0343.3741631
X-RAY DIFFRACTIONr_lrange_it6.238.84910321
X-RAY DIFFRACTIONr_ncsr_local_group_10.1080.054518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.2771390.282553X-RAY DIFFRACTION99.5562
1.59-1.6340.271310.2562459X-RAY DIFFRACTION99.8073
1.634-1.6810.2281290.2472392X-RAY DIFFRACTION99.5263
1.681-1.7330.2591160.2292366X-RAY DIFFRACTION99.5188
1.733-1.7890.2551170.232263X-RAY DIFFRACTION99.6233
1.789-1.8520.2431320.212193X-RAY DIFFRACTION99.6998
1.852-1.9220.221990.2022128X-RAY DIFFRACTION99.331
1.922-20.2341220.2072027X-RAY DIFFRACTION99.7216
2-2.0890.199980.2021950X-RAY DIFFRACTION99.5141
2.089-2.1910.2121010.2011882X-RAY DIFFRACTION99.4982
2.191-2.3090.213980.1941783X-RAY DIFFRACTION99.8408
2.309-2.4490.247930.1941686X-RAY DIFFRACTION99.7757
2.449-2.6180.202750.1961612X-RAY DIFFRACTION99.8225
2.618-2.8270.192720.191486X-RAY DIFFRACTION99.6801
2.827-3.0950.207560.1961368X-RAY DIFFRACTION99.7199
3.095-3.4590.201530.1841265X-RAY DIFFRACTION99.8485
3.459-3.9910.152620.1561093X-RAY DIFFRACTION99.7409
3.991-4.880.165520.148932X-RAY DIFFRACTION99.3939
4.88-6.8670.224460.189710X-RAY DIFFRACTION99.6047
6.867-36.880.174190.215424X-RAY DIFFRACTION99.1051

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