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- PDB-6z4k: A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone d... -

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Basic information

Entry
Database: PDB / ID: 6z4k
TitleA4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 6 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
Chem-Q7N / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 13, 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)32,68410
Polymers31,7112
Non-polymers9738
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-115 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.240, 68.320, 50.980
Angle α, β, γ (deg.)90.000, 106.170, 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-Q7N / ~{N}-[(3-methoxyphenyl)methyl]-2-selanyl-benzamide


Mass: 320.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15NO2Se / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
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: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 14, 2019 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.45→34.33 Å / Num. obs: 44385 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.029 / Rrim(I) all: 0.042 / Net I/σ(I): 13.3
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2224 / CC1/2: 0.609 / Rpim(I) all: 0.524 / Rrim(I) all: 0.769 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UXM
Resolution: 1.45→34.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.707 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2092 2240 5.049 %
Rwork0.1947 42122 -
all0.195 --
obs-44362 99.359 %
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: 20.308 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å2-0.209 Å2
2---0.963 Å20 Å2
3----0.296 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 44 232 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132331
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172107
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.653157
X-RAY DIFFRACTIONr_angle_other_deg1.6441.6074905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2045319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52924.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31115367
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg32.139152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.259158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
X-RAY DIFFRACTIONr_nbd_refined0.270.2692
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22066
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21124
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.247
X-RAY DIFFRACTIONr_metal_ion_refined0.2280.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3410.260
X-RAY DIFFRACTIONr_nbd_other0.2370.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2640.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0810.21
X-RAY DIFFRACTIONr_mcbond_it1.9131.9881255
X-RAY DIFFRACTIONr_mcbond_other1.9121.9881254
X-RAY DIFFRACTIONr_mcangle_it2.6642.9811577
X-RAY DIFFRACTIONr_mcangle_other2.6642.9811578
X-RAY DIFFRACTIONr_scbond_it3.0292.2911076
X-RAY DIFFRACTIONr_scbond_other3.012.291073
X-RAY DIFFRACTIONr_scangle_it4.4823.2961578
X-RAY DIFFRACTIONr_scangle_other4.4763.2951577
X-RAY DIFFRACTIONr_lrange_it5.28839.05610097
X-RAY DIFFRACTIONr_lrange_other5.19238.7769885
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.054580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.2941580.3143109X-RAY DIFFRACTION99.3311
1.488-1.5280.3061410.2923065X-RAY DIFFRACTION99.38
1.528-1.5730.2751670.2692902X-RAY DIFFRACTION99.5782
1.573-1.6210.2841610.2622862X-RAY DIFFRACTION99.6374
1.621-1.6740.2981610.2542773X-RAY DIFFRACTION99.6603
1.674-1.7330.3081420.2492676X-RAY DIFFRACTION99.4705
1.733-1.7980.2591470.2272584X-RAY DIFFRACTION99.4175
1.798-1.8710.2351410.2132476X-RAY DIFFRACTION99.4679
1.871-1.9540.2251190.2022386X-RAY DIFFRACTION99.2079
1.954-2.050.2331270.1862290X-RAY DIFFRACTION99.0574
2.05-2.160.1711000.1812177X-RAY DIFFRACTION99.6499
2.16-2.2910.198950.1862077X-RAY DIFFRACTION98.9522
2.291-2.4490.2171030.1831931X-RAY DIFFRACTION99.0263
2.449-2.6450.211880.1921793X-RAY DIFFRACTION99.2089
2.645-2.8960.2081010.1961674X-RAY DIFFRACTION99.4398
2.896-3.2370.204810.1771497X-RAY DIFFRACTION99.3077
3.237-3.7350.163850.1681314X-RAY DIFFRACTION99.1495
3.735-4.5670.146550.1431142X-RAY DIFFRACTION99.1715
4.567-6.4310.207490.183884X-RAY DIFFRACTION99.361
6.431-34.3490.201190.205510X-RAY DIFFRACTION98.8785

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