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- PDB-3gzp: HUMAN SOD1 G93A Metal-free Variant -

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Basic information

Entry
Database: PDB / ID: 3gzp
TitleHUMAN SOD1 G93A 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 / 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 / retina homeostasis / superoxide anion generation / 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 / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / 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 / glutathione metabolic process / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / determination of adult lifespan / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / 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 / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / 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: 3.1 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)63,3664
Polymers63,3664
Non-polymers00
Water00
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,6832
Polymers31,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-12 kcal/mol
Surface area13920 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,6832
Polymers31,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-11 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.803, 67.917, 80.962
Angle α, β, γ (deg.)90.00, 110.86, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:66 )
211chain B and (resseq 1:66 )
311chain C and (resseq 1:66 )
411chain D and (resseq 1:66 )
112chain A and (resseq 79:124 )
212chain B and (resseq 79:124 )
312chain C and (resseq 79:124 )
412chain D and (resseq 79:124 )
113chain A and (resseq 140:153 )
213chain B and (resseq 140:153 )
313chain C and (resseq 140:153 )
413chain D and (resseq 140:153 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15841.586 Da / Num. of mol.: 4 / Mutation: G93A
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

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M ammonium sulfate, 0.1 M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.03 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 11514 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.145 / Net I/σ(I): 8.2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1118 / Rsym value: 0.449 / % possible all: 95.7

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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 1HL5

1hl5


Resolution: 3.1→41.941 Å / SU ML: 2.42 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 516 5.03 %RANDOM
Rwork0.2025 ---
obs0.2048 10253 96.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.4 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1--10.5481 Å20 Å2-2.2118 Å2
2--9.557 Å20 Å2
3---0.9911 Å2
Refinement stepCycle: LAST / Resolution: 3.1→41.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 0 0 4044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.958
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A485X-RAY DIFFRACTIONPOSITIONAL
12B485X-RAY DIFFRACTIONPOSITIONAL0.023
13C485X-RAY DIFFRACTIONPOSITIONAL0.035
14D485X-RAY DIFFRACTIONPOSITIONAL0.034
21A337X-RAY DIFFRACTIONPOSITIONAL
22B337X-RAY DIFFRACTIONPOSITIONAL0.023
23C337X-RAY DIFFRACTIONPOSITIONAL0.035
24D337X-RAY DIFFRACTIONPOSITIONAL0.034
31A90X-RAY DIFFRACTIONPOSITIONAL
32B90X-RAY DIFFRACTIONPOSITIONAL0.025
33C90X-RAY DIFFRACTIONPOSITIONAL0.037
34D90X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.4120.31471240.23222289X-RAY DIFFRACTION92
3.412-3.90540.24111300.19652434X-RAY DIFFRACTION97
3.9054-4.91920.21951290.17182466X-RAY DIFFRACTION98
4.9192-41.94470.22821330.21252548X-RAY DIFFRACTION99

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