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- PDB-3gzo: HUMAN SOD1 G93A Variant -

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Basic information

Entry
Database: PDB / ID: 3gzo
TitleHUMAN SOD1 G93A Variant
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / HUMAN CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / DISEASE MUTATION / Disulfide bond / Phosphoprotein
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / 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 / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / 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 / 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 / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / 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 / response to heat / protein-folding chaperone binding / 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
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
COPPER (II) ION / MALONATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGalaleldeen, A. / Taylor, A.B. / Narayana, N. / 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: Non-polymer description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

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]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,25233
Polymers158,67610
Non-polymers1,57623
Water29,2021621
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0857
Polymers31,7352
Non-polymers3505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-16 kcal/mol
Surface area13960 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9936
Polymers31,7352
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-14 kcal/mol
Surface area13870 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9936
Polymers31,7352
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-14 kcal/mol
Surface area13850 Å2
MethodPISA
4
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0957
Polymers31,7352
Non-polymers3605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area13930 Å2
MethodPISA
5
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0857
Polymers31,7352
Non-polymers3505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-15 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.148, 203.263, 143.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15867.624 Da / Num. of mol.: 10 / 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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Non-polymers , 5 types, 1644 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1621 / 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: 3.81 Å3/Da / Density % sol: 67.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.4 M sodium malonate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 9, 2003 / Details: mirrors
RadiationMonochromator: confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 140272 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.121 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 13842 / Rsym value: 0.508 / % possible all: 99.6

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Processing

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

1sos


Resolution: 2.1→41.492 Å / SU ML: 1.75 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 6759 4.99 %RANDOM
Rwork0.1716 ---
obs0.1737 135446 96.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.4361 Å20 Å20 Å2
2---2.0683 Å20 Å2
3---3.2778 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 39 1621 12800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12430.29552010.25224007X-RAY DIFFRACTION91
2.1243-2.14930.29892100.24434129X-RAY DIFFRACTION93
2.1493-2.17560.2672140.24184091X-RAY DIFFRACTION93
2.1756-2.20310.27232230.23624143X-RAY DIFFRACTION94
2.2031-2.23210.27592320.24024159X-RAY DIFFRACTION94
2.2321-2.26270.27882370.22834163X-RAY DIFFRACTION94
2.2627-2.2950.27611870.22084156X-RAY DIFFRACTION94
2.295-2.32920.24762210.21164183X-RAY DIFFRACTION94
2.3292-2.36560.28282130.22024220X-RAY DIFFRACTION95
2.3656-2.40440.2752210.21444189X-RAY DIFFRACTION95
2.4044-2.44590.25342480.21394203X-RAY DIFFRACTION95
2.4459-2.49030.27662290.2094242X-RAY DIFFRACTION96
2.4903-2.53820.26252140.20764276X-RAY DIFFRACTION96
2.5382-2.590.24752570.2034208X-RAY DIFFRACTION96
2.59-2.64630.25672430.20024238X-RAY DIFFRACTION96
2.6463-2.70790.25682170.19654238X-RAY DIFFRACTION96
2.7079-2.77560.24392170.18164338X-RAY DIFFRACTION97
2.7756-2.85060.21682190.17734323X-RAY DIFFRACTION97
2.8506-2.93450.20712230.18124350X-RAY DIFFRACTION98
2.9345-3.02920.21412430.17114332X-RAY DIFFRACTION98
3.0292-3.13740.21952410.16044368X-RAY DIFFRACTION98
3.1374-3.2630.19152200.15074374X-RAY DIFFRACTION99
3.263-3.41140.18092370.14014414X-RAY DIFFRACTION99
3.4114-3.59120.18232420.13824398X-RAY DIFFRACTION99
3.5912-3.8160.16112310.134455X-RAY DIFFRACTION99
3.816-4.11040.16292170.12224430X-RAY DIFFRACTION99
4.1104-4.52360.14382310.11474469X-RAY DIFFRACTION99
4.5236-5.17710.13982280.124458X-RAY DIFFRACTION99
5.1771-6.51850.1752170.14464508X-RAY DIFFRACTION99
6.5185-41.50060.19772260.16684625X-RAY DIFFRACTION98

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