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- PDB-4nin: DSVISLS segment 101-107 from Human Superoxide Dismutase -

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Basic information

Entry
Database: PDB / ID: 4nin
TitleDSVISLS segment 101-107 from Human Superoxide Dismutase
ComponentsDSVISLS 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 / glutathione metabolic process / axon cytoplasm / 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 / locomotory behavior / regulation of mitochondrial membrane potential / 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: 1.402 Å
AuthorsSievers, S.A. / Sawaya, M.R. / Eisenberg, D.
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DSVISLS segment from Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7852
Polymers7201
Non-polymers651
Water724
1
A: DSVISLS segment from Superoxide dismutase [Cu-Zn]
hetero molecules
x 10


Theoretical massNumber of molelcules
Total (without water)7,85220
Polymers7,19810
Non-polymers65410
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_654x+1,y,z-11
crystal symmetry operation1_754x+2,y,z-11
crystal symmetry operation1_354x-2,y,z-11
crystal symmetry operation1_454x-1,y,z-11
Unit cell
Length a, b, c (Å)4.805, 45.337, 11.300
Angle α, β, γ (deg.)90.000, 100.520, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a pair of beta-sheets formed by the symmetry operators X,Y,Z and X,Y,Z-1 with positive and negative unit cell translations along the x axis. For example one sheet is composed of symmetry operators X,Y,Z; X+1,Y,Z; X-1,Y,Z; X+2,Y,Z; X-2,Y,Z: the opposing sheet is composed of symmetry operators X,Y,Z-1; X+1,Y,Z-1; X-1,Y,Z-1; X+2,Y,Z-1; X-2,Y,Z-1, etc.

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Components

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


Mass: 719.783 Da / Num. of mol.: 1 / Fragment: UNP residues 102-108 / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: P00441
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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: 1.68 Å3/Da / Density % sol: 26.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH 6.0, 20% PEG 6000, and 5 mM ZnCl2, 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: Jul 22, 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: 1.4→100 Å / Num. all: 717 / Num. obs: 717 / % possible obs: 73.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 11.41 Å2 / Rmerge(I) obs: 0.186 / Χ2: 1.087 / Net I/σ(I): 24.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.511.50.166570.917128.4
1.51-1.661.80.2741211.343159.3
1.66-1.92.80.2771551.055188.1
1.9-2.394.20.2651931.103196
2.39-1005.70.1691911.065199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.61 Å22.76 Å
Translation1.61 Å22.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.402→22.669 Å / Occupancy max: 1 / Occupancy min: 0.55 / FOM work R set: 0.7046 / SU ML: 0 / σ(F): 1.66 / Phase error: 34.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 65 9.22 %RANDOM
Rwork0.1872 ---
obs0.1911 705 74.05 %-
all-705 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.791 Å2 / ksol: 0.435 e/Å3
Displacement parametersBiso max: 28.39 Å2 / Biso mean: 19.2775 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1--4.9106 Å2-0 Å2-2.585 Å2
2---5.6507 Å20 Å2
3---10.5613 Å2
Refinement stepCycle: LAST / Resolution: 1.402→22.669 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms50 0 1 4 55
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00649
X-RAY DIFFRACTIONf_angle_d0.92366
X-RAY DIFFRACTIONf_chiral_restr0.06110
X-RAY DIFFRACTIONf_plane_restr0.0028
X-RAY DIFFRACTIONf_dihedral_angle_d10.20517
LS refinement shellResolution: 1.4023→22.6715 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2281 65 -
Rwork0.1872 640 -
all-705 -
obs--74 %

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