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- PDB-6z4j: A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone d... -

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Basic information

Entry
Database: PDB / ID: 6z4j
TitleA4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 5 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 / 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
~{N}-[(3-chlorophenyl)methyl]-2-selanyl-benzamide / 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 6, 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)32,69310
Polymers31,7112
Non-polymers9828
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-114 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.495, 68.321, 51.321
Angle α, β, γ (deg.)90.000, 106.362, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-Q7W / ~{N}-[(3-chlorophenyl)methyl]-2-selanyl-benzamide


Mass: 324.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12ClNOSe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mM NaOAc pH 4.7, 150mM NaCl, 2.5M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 14, 2020 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→36.964 Å / Num. obs: 36977 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.407 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.04 / Rrim(I) all: 0.058 / Net I/σ(I): 11.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2 / Num. unique obs: 1794 / CC1/2: 0.887 / Rpim(I) all: 0.25 / Rrim(I) all: 0.376 / % possible all: 99.6

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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: 1.55→36.964 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.813 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2077 1835 4.966 %
Rwork0.1891 35113 -
all0.19 --
obs-36948 99.779 %
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: 21.058 Å2
Baniso -1Baniso -2Baniso -3
1-1.165 Å20 Å2-0.19 Å2
2---0.987 Å20 Å2
3----0.056 Å2
Refinement stepCycle: LAST / Resolution: 1.55→36.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 42 166 2409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132378
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172155
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.653223
X-RAY DIFFRACTIONr_angle_other_deg1.5771.6055023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.225325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21524.257101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36715381
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg35.286152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.587158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022803
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02459
X-RAY DIFFRACTIONr_nbd_refined0.2560.2603
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21998
X-RAY DIFFRACTIONr_nbtor_refined0.160.21109
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21106
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.232
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3520.239
X-RAY DIFFRACTIONr_nbd_other0.2820.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.24
X-RAY DIFFRACTIONr_mcbond_it22.0331279
X-RAY DIFFRACTIONr_mcbond_other22.0361280
X-RAY DIFFRACTIONr_mcangle_it2.8333.0531613
X-RAY DIFFRACTIONr_mcangle_other2.8323.0491613
X-RAY DIFFRACTIONr_scbond_it3.2222.4271099
X-RAY DIFFRACTIONr_scbond_other3.2212.431100
X-RAY DIFFRACTIONr_scangle_it4.7353.4661610
X-RAY DIFFRACTIONr_scangle_other4.7333.4691611
X-RAY DIFFRACTIONr_lrange_it5.74939.8569918
X-RAY DIFFRACTIONr_lrange_other5.7139.6819793
X-RAY DIFFRACTIONr_ncsr_local_group_10.090.054591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.2571390.242571X-RAY DIFFRACTION99.486
1.59-1.6340.231380.2242496X-RAY DIFFRACTION99.6595
1.634-1.6810.2151270.2162457X-RAY DIFFRACTION99.7298
1.681-1.7330.2541160.1982360X-RAY DIFFRACTION99.8387
1.733-1.7890.2481210.2052326X-RAY DIFFRACTION100
1.789-1.8520.2581280.1962231X-RAY DIFFRACTION99.8307
1.852-1.9220.2221040.1912172X-RAY DIFFRACTION99.8684
1.922-20.2251210.1882052X-RAY DIFFRACTION99.5419
2-2.0890.2281020.192002X-RAY DIFFRACTION99.905
2.089-2.1910.2091000.1921925X-RAY DIFFRACTION99.9013
2.191-2.3090.2141000.191795X-RAY DIFFRACTION99.8419
2.309-2.4490.228940.1841714X-RAY DIFFRACTION99.7793
2.449-2.6180.196800.1951615X-RAY DIFFRACTION99.8821
2.618-2.8270.196690.1911508X-RAY DIFFRACTION99.747
2.827-3.0950.163600.1891408X-RAY DIFFRACTION99.9319
3.095-3.4590.209550.1851273X-RAY DIFFRACTION99.8496
3.459-3.9910.166630.171114X-RAY DIFFRACTION100
3.991-4.880.193500.158940X-RAY DIFFRACTION99.7984
4.88-6.8670.203490.197727X-RAY DIFFRACTION100
6.867-36.9640.217190.212427X-RAY DIFFRACTION98.2379

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