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- PDB-5wmj: KVWGSI segment from Superoxide Dismutase 1,residues 30-35 -

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Basic information

Entry
Database: PDB / ID: 5wmj
TitleKVWGSI segment from Superoxide Dismutase 1,residues 30-35
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
trifluoroacetic acid / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSangwan, S. / Sawaya, M. / Eisenberg, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)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
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 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 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)1,4943
Polymers1,3802
Non-polymers1141
Water1086
1
A: Superoxide dismutase [Cu-Zn]

A: Superoxide dismutase [Cu-Zn]

A: Superoxide dismutase [Cu-Zn]

A: Superoxide dismutase [Cu-Zn]

B: Superoxide dismutase [Cu-Zn]
hetero molecules

B: Superoxide dismutase [Cu-Zn]
hetero molecules

B: Superoxide dismutase [Cu-Zn]
hetero molecules

B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,97512
Polymers5,5198
Non-polymers4564
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation1_655x+1,y,z2
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
crystal symmetry operation4_645x+3/2,-y-1/2,-z1
crystal symmetry operation4_535x+1/2,-y-3/2,-z1
crystal symmetry operation4_635x+3/2,-y-3/2,-z1
Unit cell
Length a, b, c (Å)9.518, 20.282, 44.249
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: 689.823 Da / Num. of mol.: 2 / Fragment: UNP residues 31-36 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.55 Å3/Da / Density % sol: 20.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Reservoir solution contained 4M Sodium Formate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 1738 / % possible obs: 89.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.166 / Χ2: 1.012 / Net I/σ(I): 4.6 / Num. measured all: 11623
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.4-1.453.10.551320.986175
1.45-1.5130.4781410.705177
1.51-1.5850.5031680.873184.4
1.58-1.666.10.4261650.816191.2
1.66-1.766.20.3761700.732195
1.76-1.980.3281820.853189.2
1.9-2.0990.1821731.093194.5
2.09-2.398.60.1591871.147193.5
2.39-3.028.40.1561931.092196.5
3.02-1007.20.0792271.282197

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
SCALEPACK1.98.7data scaling
PHASER2.52phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2 ANTI-PARALLEL BETA STRANDS

Resolution: 1.4→22.12 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1566 / WRfactor Rwork: 0.1474 / FOM work R set: 0.8693 / SU B: 1.26 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0866 / SU Rfree: 0.0714 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 157 9.1 %RANDOM
Rwork0.1707 ---
obs0.1706 1564 89.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 26.04 Å2 / Biso mean: 5.399 Å2 / Biso min: 2.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.34 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.4→22.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms98 0 7 7 112
Biso mean--12.58 17.75 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02120
X-RAY DIFFRACTIONr_bond_other_d0.0010.02111
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.913165
X-RAY DIFFRACTIONr_angle_other_deg0.6293253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.078512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.21203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.81519
X-RAY DIFFRACTIONr_chiral_restr0.1960.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02119
X-RAY DIFFRACTIONr_gen_planes_other00.0229
LS refinement shellResolution: 1.398→1.434 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 5 -
Rwork0.28 77 -
all-82 -
obs--64.57 %

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