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- PDB-4nip: GVIGIAQ segment 147-153 from Human Superoxide Dismutase -

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Basic information

Entry
Database: PDB / ID: 4nip
TitleGVIGIAQ segment 147-153 from Human Superoxide Dismutase
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 / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / cellular response to cadmium ion / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / glutathione metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / response to amphetamine / thymus development / positive regulation of cytokine production / placenta development / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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-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: 1.9 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 / 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: GVTGIAQ segment from Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)6571
Polymers6571
Non-polymers00
Water543
1
A: GVTGIAQ segment from Superoxide dismutase [Cu-Zn]
x 10


Theoretical massNumber of molelcules
Total (without water)6,56810
Polymers6,56810
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)50.128, 4.843, 18.142
Angle α, β, γ (deg.)90.000, 99.500, 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: 656.772 Da / Num. of mol.: 1 / Fragment: UNP Residues 148-154 / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: P00441
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.65 Å3/Da / Density % sol: 25.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1 M sodium acetate pH 4.5, 1.75 M ammonium sulfate, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.895432 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 13, 2007
RadiationMonochromator: cryogenically-cooled single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895432 Å / Relative weight: 1
ReflectionResolution: 1.9→90 Å / Num. all: 415 / Num. obs: 415 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.144 / Χ2: 1.515 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-2.052.40.206741.865189.2
2.05-2.252.50.228901.872196.8
2.25-2.582.40.204771.056191.7
2.58-3.252.50.196701.582197.2
3.25-902.30.1111041.1961100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å24.86 Å
Translation2.3 Å24.86 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→24.85 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2872 / WRfactor Rwork: 0.241 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8529 / SU B: 3.436 / SU ML: 0.104 / SU R Cruickshank DPI: 0.2405 / SU Rfree: 0.1787 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 43 10.2 %RANDOM
Rwork0.2321 ---
obs0.2339 378 96.12 %-
all-378 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 40.82 Å2 / Biso mean: 17.1302 Å2 / Biso min: 2.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å2-0.74 Å2
2---2.33 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.85 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms46 0 0 3 49
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02245
X-RAY DIFFRACTIONr_bond_other_d0.0010.0226
X-RAY DIFFRACTIONr_angle_refined_deg1.3162.00860
X-RAY DIFFRACTIONr_angle_other_deg0.734366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.28656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.639301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.609157
X-RAY DIFFRACTIONr_chiral_restr0.090.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0250
X-RAY DIFFRACTIONr_gen_planes_other00.026
X-RAY DIFFRACTIONr_nbd_refined0.0850.22
X-RAY DIFFRACTIONr_nbd_other0.1860.217
X-RAY DIFFRACTIONr_nbtor_refined0.1420.219
X-RAY DIFFRACTIONr_nbtor_other0.0680.224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.26
X-RAY DIFFRACTIONr_mcbond_it6.377244
X-RAY DIFFRACTIONr_mcbond_other2.278215
X-RAY DIFFRACTIONr_mcangle_it5.949351
X-RAY DIFFRACTIONr_scbond_it4.287213
X-RAY DIFFRACTIONr_scangle_it3.15839
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.509 2 -
Rwork0.264 26 -
all-28 -
obs--96.55 %

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