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- PDB-6b79: Curved pair of sheets formed from SOD1 residues 28-38 with famili... -

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Basic information

Entry
Database: PDB / ID: 6b79
TitleCurved pair of sheets formed from SOD1 residues 28-38 with familial mutation G37R.
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsPROTEIN FIBRIL / amyloid fibril
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
Chem-ORA / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
Model detailsamyloid-related oligomer
AuthorsSangwan, S. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)ag054022 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Protein Sci. / Year: 2018
Title: Atomic structures of corkscrew-forming segments of SOD1 reveal varied oligomer conformations.
Authors: Sangwan, S. / Sawaya, M.R. / Murray, K.A. / Hughes, M.P. / Eisenberg, D.S.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1973
Polymers2,7892
Non-polymers4081
Water28816
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules

A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules

A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules

A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,79012
Polymers11,1568
Non-polymers1,6344
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation2_565-x,y+1,-z1
Unit cell
Length a, b, c (Å)56.940, 11.640, 44.930
Angle α, β, γ (deg.)90.000, 127.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 1394.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-ORA / 7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid / Orange G / Orange G


Mass: 408.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12N2O7S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES pH 7.5, Sodium citrate, 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→35.73 Å / Num. obs: 2330 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.088 % / Biso Wilson estimate: 28.25 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.211 / Χ2: 0.889 / Net I/σ(I): 4.06 / Num. measured all: 7194 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.842.4031.5790.481290.2151.97974.1
1.84-1.892.5890.8740.961580.4631.0994
1.89-1.952.8550.8041.321790.5860.98698.9
1.95-2.013.1580.61.71460.7070.72798.6
2.01-2.073.3560.5682.031460.6050.678100
2.07-2.153.2620.4822.31450.7420.58199.3
2.15-2.233.340.4082.871530.8420.48899.4
2.23-2.323.2210.2913.61400.8790.352100
2.32-2.423.3110.3033.651350.8730.36597.1
2.42-2.543.2950.2364.071220.9520.284100
2.54-2.683.240.2643.921210.9350.322100
2.68-2.843.2460.2054.991260.9370.247100
2.84-3.043.280.1296.381070.9890.15495.5
3.04-3.283.040.1047.56990.9830.12899
3.28-3.593.1960.1217.851020.980.14598.1
3.59-4.023.1290.0998.54850.980.11797.7
4.02-4.643.0540.0919.22740.9770.10897.4
4.64-5.6830.1268.93770.9670.15198.7
5.68-8.032.7020.0868.78470.990.10395.9
8.03-35.732.5640.0689.08390.9820.09195.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
BUSTER2.10.0refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DLI

5dli


Resolution: 1.8→35.73 Å / Cor.coef. Fo:Fc: 0.9087 / Cor.coef. Fo:Fc free: 0.9164 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.267 223 9.58 %RANDOM
Rwork0.2303 ---
obs0.2337 2327 97.9 %-
Displacement parametersBiso max: 88.55 Å2 / Biso mean: 30.08 Å2 / Biso min: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.9875 Å20 Å27.2771 Å2
2--7.0883 Å20 Å2
3----1.1008 Å2
Refine analyzeLuzzati coordinate error obs: 0.298 Å
Refinement stepCycle: final / Resolution: 1.8→35.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms188 0 27 16 231
Biso mean--24.65 35.77 -
Num. residues----22
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d80SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes2HARMONIC2
X-RAY DIFFRACTIONt_gen_planes29HARMONIC5
X-RAY DIFFRACTIONt_it219HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion22SEMIHARMONIC5
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_contact274SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d219HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg294HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion17.03
LS refinement shellResolution: 1.8→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3159 62 9.97 %
Rwork0.2727 560 -
all0.2764 622 -
obs--97.9 %

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