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- PDB-5dli: Corkscrew assembly of SOD1 residues 28-38 -

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Basic information

Entry
Database: PDB / ID: 5dli
TitleCorkscrew assembly of SOD1 residues 28-38
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsUNKNOWN FUNCTION / amyloid-related oligomer
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 / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...action potential initiation / neurofilament cytoskeleton organization / 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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / 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 / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / 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
IODIDE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
Model detailsamyloid-related oligomer
AuthorsSangwan, S. / Zhao, A. / Sawaya, M.R. / Eisenberg, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG04812 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Atomic structure of a toxic, oligomeric segment of SOD1 linked to amyotrophic lateral sclerosis (ALS).
Authors: Sangwan, S. / Zhao, A. / Adams, K.L. / Jayson, C.K. / Sawaya, M.R. / Guenther, E.L. / Pan, A.C. / Ngo, J. / Moore, D.M. / Soriaga, A.B. / Do, T.D. / Goldschmidt, L. / Nelson, R. / Bowers, M. ...Authors: Sangwan, S. / Zhao, A. / Adams, K.L. / Jayson, C.K. / Sawaya, M.R. / Guenther, E.L. / Pan, A.C. / Ngo, J. / Moore, D.M. / Soriaga, A.B. / Do, T.D. / Goldschmidt, L. / Nelson, R. / Bowers, M.T. / Koehler, C.M. / Shaw, D.E. / Novitch, B.G. / Eisenberg, D.S.
History
DepositionSep 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,08611
Polymers9,7408
Non-polymers3463
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.090, 44.390, 71.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 1217.523 Da / Num. of mol.: 8 / Fragment: Residues 29-39 / Mutation: P29K / Source method: obtained synthetically / Details: synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: reservoir contained 13% PEG 6000, 0.2M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→19.33 Å / Num. obs: 6261 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 21.81 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.111 / Χ2: 1.084 / Net I/σ(I): 14.4 / Num. measured all: 43500
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.05 % / Rmerge F obs: 0.931 / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 4.88 / Num. possible: 875 / Num. unique obs: 856 / Rrim(I) all: 0.488 / Rejects: 0 / % possible all: 96.8

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHELXphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→19.33 Å / Cor.coef. Fo:Fc: 0.9217 / Cor.coef. Fo:Fc free: 0.9212 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.234 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.194
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 313 5.01 %RANDOM
Rwork0.2125 ---
obs0.215 6249 95.84 %-
Displacement parametersBiso max: 82.87 Å2 / Biso mean: 23.83 Å2 / Biso min: 6.35 Å2
Baniso -1Baniso -2Baniso -3
1--4.3559 Å20 Å20 Å2
2---2.3511 Å20 Å2
3---6.7071 Å2
Refine analyzeLuzzati coordinate error obs: 0.243 Å
Refinement stepCycle: final / Resolution: 2.1→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms688 0 10 50 748
Biso mean--46.3 34.29 -
Num. residues----88
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d254SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes8HARMONIC2
X-RAY DIFFRACTIONt_gen_planes91HARMONIC5
X-RAY DIFFRACTIONt_it715HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion81SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact778SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d715HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg947HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion15.32
LS refinement shellResolution: 2.1→2.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2292 87 4.98 %
Rwork0.1716 1660 -
all0.1744 1747 -
obs--95.84 %

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