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- PDB-3gzq: HUMAN SOD1 A4V Metal-free Variant -

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Basic information

Entry
Database: PDB / ID: 3gzq
TitleHUMAN SOD1 A4V Metal-free Variant
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / HUMAN CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / COPPER / ZINC / AMYOTROPHIC LATERAL SCLEROSIS / DISEASE MUTATION / ACETYLATION / CYTOPLASM / APO / Disulfide bond / Phosphoprotein / Ubl conjugation
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / regulation of organ growth / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / regulation of organ growth / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / regulation of GTPase activity / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / ectopic germ cell programmed cell death / regulation of multicellular organism growth / neuronal action potential / response to axon injury / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / thymus development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / determination of adult lifespan / positive regulation of cytokine production / locomotory behavior / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / peroxisome / Platelet degranulation / protein-folding chaperone binding / gene expression / 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 / positive regulation of apoptotic process / response to xenobiotic stimulus / 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
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / 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 (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsGalaleldeen, A. / Taylor, A.B. / Whitson, L.J. / Hart, P.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2009
Title: Structural and biophysical properties of metal-free pathogenic SOD1 mutants A4V and G93A.
Authors: Galaleldeen, A. / Strange, R.W. / Whitson, L.J. / Antonyuk, S.V. / Narayana, N. / Taylor, A.B. / Schuermann, J.P. / Holloway, S.P. / Hasnain, S.S. / Hart, P.J.
History
DepositionApr 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)31,9554
Polymers31,7632
Non-polymers1922
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-36 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.513, 58.811, 104.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15881.653 Da / Num. of mol.: 2 / Mutation: A4V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351-HSOD / Production host: saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EGY118 / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.6 M ammonium sulfate, 0.1 M MES, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 49673 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.045 / Net I/σ(I): 33.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4589 / Rsym value: 0.582 / % possible all: 93.2

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OZU

1ozu


Resolution: 1.401→30.064 Å / SU ML: 0.32 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 2518 5.09 %RANDOM
Rwork0.1644 ---
obs0.1659 49501 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.385 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.8219 Å20 Å20 Å2
2--2.847 Å20 Å2
3---0.9749 Å2
Refinement stepCycle: LAST / Resolution: 1.401→30.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 10 251 2077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg1.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.401-1.42770.25391130.21382305X-RAY DIFFRACTION89
1.4277-1.45690.19811390.18322516X-RAY DIFFRACTION97
1.4569-1.48860.2061240.16252598X-RAY DIFFRACTION99
1.4886-1.52320.18841520.14392600X-RAY DIFFRACTION100
1.5232-1.56130.17691450.13382625X-RAY DIFFRACTION100
1.5613-1.60350.17321440.12372573X-RAY DIFFRACTION100
1.6035-1.65070.15731590.12272595X-RAY DIFFRACTION100
1.6507-1.70390.17571230.11912639X-RAY DIFFRACTION100
1.7039-1.76480.15411520.12332620X-RAY DIFFRACTION100
1.7648-1.83550.17911350.12362639X-RAY DIFFRACTION100
1.8355-1.9190.18341360.13332606X-RAY DIFFRACTION99
1.919-2.02020.16171360.14042615X-RAY DIFFRACTION99
2.0202-2.14670.18071490.13152625X-RAY DIFFRACTION100
2.1467-2.31240.17551360.15562615X-RAY DIFFRACTION99
2.3124-2.5450.17491380.15642692X-RAY DIFFRACTION100
2.545-2.9130.18931330.1682671X-RAY DIFFRACTION100
2.913-3.6690.17671500.16082698X-RAY DIFFRACTION99
3.669-30.07050.20281540.17452751X-RAY DIFFRACTION97

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