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- PDB-6sph: A4V MUTANT OF HUMAN SUPEROXIDE DISMUTASE 1 WITH EBSELEN BOND IN C... -

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Basic information

Entry
Database: PDB / ID: 6sph
TitleA4V MUTANT OF HUMAN SUPEROXIDE DISMUTASE 1 WITH EBSELEN BOND IN C2 SPACE GROUP
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / A4V SOD1 mutant / MND / ALS
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / removal of superoxide radicals / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / dendrite cytoplasm / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / 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 / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
N-phenyl-2-selanylbenzamide / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsShahid, M. / Chantadul, V. / Amporndanai, K. / Wright, G. / Antonyuk, S. / Hasnain, S.
CitationJournal: Commun Biol / Year: 2020
Title: Ebselen as template for stabilization of A4V mutant dimer for motor neuron disease therapy.
Authors: Chantadul, V. / Wright, G.S.A. / Amporndanai, K. / Shahid, M. / Antonyuk, S.V. / Washbourn, G. / Rogers, M. / Roberts, N. / Pye, M. / O'Neill, P.M. / Hasnain, S.S.
History
DepositionSep 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_conn_type
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,42932
Polymers95,1346
Non-polymers3,29526
Water14,484804
1
A: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6759
Polymers31,7112
Non-polymers9637
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-26 kcal/mol
Surface area14090 Å2
MethodPISA
2
E: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,92312
Polymers31,7112
Non-polymers1,21210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-32 kcal/mol
Surface area14120 Å2
MethodPISA
3
J: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,83111
Polymers31,7112
Non-polymers1,1209
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-5 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.313, 195.237, 75.348
Angle α, β, γ (deg.)90.000, 97.860, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-391-

HOH

21E-390-

HOH

31J-538-

HOH

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Components

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Protein , 1 types, 6 molecules ACEGJL

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


Mass: 15855.613 Da / Num. of mol.: 6 / Mutation: Ala4Val
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 , 6 types, 830 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 4.3 Å3/Da / Density % sol: 71.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl pH 7.4-8.0, 2.4-2.6 M ammonium sulphate, 150 mM NaCl
PH range: 7.4-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54179 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.25→47.25 Å / Num. obs: 70706 / % possible obs: 97.3 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.3
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4822 / CC1/2: 0.639 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
AUTOMARdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UXM

1uxm


Resolution: 2.25→43 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.169
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 3894 5.2 %RANDOM
Rwork0.1859 ---
obs0.18781 70706 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.79 Å2 / Biso mean: 18.461 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.28 Å2
2---0.1 Å20 Å2
3---0.63 Å2
Refinement stepCycle: final / Resolution: 2.25→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 175 812 7659
Biso mean--30.1 40.11 -
Num. residues----918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136972
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176336
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.6469401
X-RAY DIFFRACTIONr_angle_other_deg1.2831.60214774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1015918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83124.459314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.612151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0831524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028003
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021311
X-RAY DIFFRACTIONr_mcbond_it0.7681.7883672
X-RAY DIFFRACTIONr_mcbond_other0.7681.7873671
X-RAY DIFFRACTIONr_mcangle_it1.362.6764581
LS refinement shellResolution: 2.25→2.308 Å
RfactorNum. reflection% reflection
Rfree0.327 279 -
Rwork0.277 4822 -
obs--91.86 %

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