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- PDB-4nio: GVTGIAQ segment 147-153 from Human Superoxide Dismutase with I149... -

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Basic information

Entry
Database: PDB / ID: 4nio
TitleGVTGIAQ segment 147-153 from Human Superoxide Dismutase with I149T mutation associated with a familial form of amyotrophic lateral sclerosis
ComponentsGVTGIAQ segment from Superoxide dismutase [Cu-Zn]
KeywordsPROTEIN FIBRIL / steric zipper / cross-beta spine / amyloid fiber
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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsSievers, S.A. / Sawaya, M.R. / Eisenberg, D. / Ivanova, M.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS.
Authors: Ivanova, M.I. / Sievers, S.A. / Guenther, E.L. / Johnson, L.M. / Winkler, D.D. / Galaleldeen, A. / Sawaya, M.R. / Hart, P.J. / Eisenberg, D.S.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: GVTGIAQ segment from Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)6451
Polymers6451
Non-polymers00
Water724
1
A: GVTGIAQ segment from Superoxide dismutase [Cu-Zn]
x 10


Theoretical massNumber of molelcules
Total (without water)6,44710
Polymers6,44710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_535-x+1/2,y-3/2,-z1
crystal symmetry operation4_565-x+1/2,y+3/2,-z1
crystal symmetry operation4_575-x+1/2,y+5/2,-z1
Unit cell
Length a, b, c (Å)47.787, 4.787, 17.687
Angle α, β, γ (deg.)90.000, 109.390, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a pair of beta-sheets. One sheet is composed of symmetry operators X,Y,Z; X,Y-1,Z; X,Y+1,Z; X,Y-2,Z; X,Y+2,Z, etc.: the opposing sheet is composed of symmetry operators 1/2-x,1/2+y,-z; 1/2-x,-1/2+y,-z; 1/2-x, 3/2+y,-z; 1/2-x,-3/2+y,-z; 1/2-x, 5/2+y,-z, etc.

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Components

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


Mass: 644.718 Da / Num. of mol.: 1 / Fragment: UNP Residues 148-154 / Mutation: I149T / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: P00441
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.48 Å3/Da / Density % sol: 16.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 0.7 M hexanediol, vapor diffusion, hanging drop, temperature 298K

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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: Mar 3, 2011 / Details: mirrors
RadiationMonochromator: cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. all: 1053 / Num. obs: 1053 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.042 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.352.40.269841.014181.6
1.35-1.42.70.311951.058192.2
1.4-1.463.20.2851001.012196.2
1.46-1.543.70.3531111.064194.1
1.54-1.644.30.2621071.099195.5
1.64-1.765.20.211911.0291100
1.76-1.945.40.1761021.019199
1.94-2.225.40.1451281.0341100
2.22-2.85.10.1291021.064199
2.8-10050.0931331.023198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å16.68 Å
Translation1.6 Å16.68 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→22.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2247 / WRfactor Rwork: 0.2221 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7612 / SU B: 1.39 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0712 / SU Rfree: 0.0731 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 116 11 %RANDOM
Rwork0.2018 ---
obs0.2051 1053 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 31.56 Å2 / Biso mean: 9.1706 Å2 / Biso min: 5.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.46 Å2
2---0.24 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.3→22.54 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms45 0 0 4 49
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02244
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.98659
X-RAY DIFFRACTIONr_angle_other_deg0.611361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.167301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg3.5156
X-RAY DIFFRACTIONr_chiral_restr0.0630.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0250
X-RAY DIFFRACTIONr_gen_planes_other00.026
X-RAY DIFFRACTIONr_mcbond_it0.5341.533
X-RAY DIFFRACTIONr_mcbond_other0.0711.515
X-RAY DIFFRACTIONr_mcangle_it0.894251
X-RAY DIFFRACTIONr_scbond_it0.64311
X-RAY DIFFRACTIONr_scangle_it1.2614.58
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.539 7 -
Rwork0.236 51 -
all-58 -
obs--81.69 %

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