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- PDB-6foi: Human Cys57/156Ala superoxide dismutase-1 (SOD1), as isolated. -

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Basic information

Entry
Database: PDB / ID: 6foi
TitleHuman Cys57/156Ala superoxide dismutase-1 (SOD1), as isolated.
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / zinc / copper / disulphide mutant
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / cellular response to cadmium ion / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / glutathione metabolic process / 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 / positive regulation of phagocytosis / response to amphetamine / thymus development / positive regulation of cytokine production / placenta development / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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-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 / Resolution: 2 Å
AuthorsWright, G.S.A. / Sala, F.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
Funding support United Kingdom, Brazil, 6items
OrganizationGrant numberCountry
Motor Neurone Disease AssociationHasnain/Apr15/833-791 United Kingdom
Medical Research Council (United Kingdom)MRF-060-0002-RG-HASNA United Kingdom
Sao Paulo Research Fundation2015/00062-1 Brazil
Sao Paulo Research Fundation2016/24686-7 Brazil
National Council for Scientific and Technological Development407438/2013-0 Brazil
National Council for Scientific and Technological Development (CNPq)407438/2013-0 Brazil
CitationJournal: Plos Biol. / Year: 2019
Title: Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS.
Authors: Sala, F.A. / Wright, G.S.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
History
DepositionFeb 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
M: Superoxide dismutase [Cu-Zn]
O: Superoxide dismutase [Cu-Zn]
Q: Superoxide dismutase [Cu-Zn]
S: Superoxide dismutase [Cu-Zn]
U: Superoxide dismutase [Cu-Zn]
W: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,19537
Polymers189,16112
Non-polymers2,03425
Water19,1681064
1
A: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9467
Polymers31,5272
Non-polymers4195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-41 kcal/mol
Surface area13990 Å2
MethodPISA
2
D: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8506
Polymers31,5272
Non-polymers3234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-42 kcal/mol
Surface area14190 Å2
MethodPISA
3
I: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8506
Polymers31,5272
Non-polymers3234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-44 kcal/mol
Surface area14030 Å2
MethodPISA
4
M: Superoxide dismutase [Cu-Zn]
O: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7545
Polymers31,5272
Non-polymers2273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-34 kcal/mol
Surface area14080 Å2
MethodPISA
5
Q: Superoxide dismutase [Cu-Zn]
S: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9467
Polymers31,5272
Non-polymers4195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-50 kcal/mol
Surface area13910 Å2
MethodPISA
6
U: Superoxide dismutase [Cu-Zn]
W: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8506
Polymers31,5272
Non-polymers3234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-45 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.650, 162.959, 174.601
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] / Superoxide dismutase 1 / hSod1


Mass: 15763.432 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1064 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Lithium sulphate 24% w/v PEG 4000 0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→81.48 Å / Num. obs: 144348 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.056 / Rrim(I) all: 0.102 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7089 / CC1/2: 0.783 / Rrim(I) all: 0.101 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c9v

2c9v


Resolution: 2→81.48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.245 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.171
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT USED THROUGHOUT. ALL CHAINS WERE NCS RESTRAINED TO CHAIN F IN EARLY STAGES.
RfactorNum. reflection% reflectionSelection details
Rfree0.25941 7261 5 %RANDOM
Rwork0.22076 ---
obs0.2227 136979 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--2.34 Å20 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 2→81.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13259 0 77 1064 14400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01913567
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212348
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.94718334
X-RAY DIFFRACTIONr_angle_other_deg0.841328796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17951833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4025.571578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.013152183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5821550
X-RAY DIFFRACTIONr_chiral_restr0.0640.22032
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022473
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0830.7267341
X-RAY DIFFRACTIONr_mcbond_other0.0830.7267340
X-RAY DIFFRACTIONr_mcangle_it0.1521.0899159
X-RAY DIFFRACTIONr_mcangle_other0.1521.0899160
X-RAY DIFFRACTIONr_scbond_it0.1660.7716226
X-RAY DIFFRACTIONr_scbond_other0.1130.766212
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.1351.1389153
X-RAY DIFFRACTIONr_long_range_B_refined7.1210.21714185
X-RAY DIFFRACTIONr_long_range_B_other7.0369.35513955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 579 -
Rwork0.306 10011 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.84120.368-0.39972.4714-1.33783.37660.02340.00250.15880.0584-0.0839-0.038-0.33280.10760.06040.1765-0.0102-0.03710.20590.02280.290923.607842.518415.4422
21.6548-0.0742-0.2433.57590.42572.19870.0026-0.05020.209-0.454-0.00440.1513-0.2034-0.05830.00180.19410.0114-0.02450.2344-0.01660.3487-13.119948.97720.6001
32.1982-0.3428-0.05592.1807-0.97933.00710.0432-0.1396-0.1123-0.007-0.0330.05910.0416-0.0767-0.01030.0020.002700.2490.05020.298721.275820.602632.3746
42.09340.3003-0.70522.8868-0.20071.5803-0.0274-0.28980.1163-0.08840.0339-0.08950.05160.1682-0.00650.00930.041-0.00310.35640.04680.2477-15.603323.058630.4817
51.3115-0.2424-0.184.75660.37963.05180.35870.2742-0.1369-0.8609-0.326-0.561-0.09430.0227-0.03280.59610.22930.09430.38550.05420.470121.9944-37.068228.67
62.0596-0.18830.83184.6455-0.58551.70.3387-0.079-0.0714-0.6053-0.4572-0.57530.31180.0810.11860.25260.09820.10220.33880.1640.329520.4239-11.151338.5848
72.1501-0.0948-0.66583.15920.76563.52940.0576-0.33050.21210.3098-0.0616-0.2382-0.29380.01420.0040.1855-0.0327-0.06320.45390.0540.271314.91679.961762.1134
82.83820.1132-0.41053.31020.42412.45630.0549-0.86690.23450.7333-0.1186-0.1643-0.2265-0.0980.06370.6623-0.0407-0.10581.0555-0.04410.27127.836113.461288.6088
94.52710.20210.79082.7787-1.02422.98650.0862-0.9438-0.31850.1759-0.03190.09670.1993-0.2644-0.05440.12940.01210.03330.57770.08490.2279-20.55212.085354.0808
102.7111-0.27630.23922.281-0.29945.22070.0062-0.2932-0.03140.1115-0.02140.18730.1448-0.53690.01520.4372-0.02850.07380.59330.0250.3934-25.2558-0.419981.4884
112.3083-1.28880.68473.7155-0.17063.0850.10010.4387-0.6309-0.3381-0.05240.1690.8363-0.0886-0.04770.81940.038-0.08560.553-0.12930.6931-6.619-28.38766.5199
121.9598-0.82260.1881.57380.33114.31380.27280.4525-0.2604-0.3438-0.23920.15520.4735-0.1404-0.03360.37550.1131-0.09050.4328-0.01270.3581-13.4209-7.937224.0597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 153
2X-RAY DIFFRACTION2D1 - 153
3X-RAY DIFFRACTION3F1 - 153
4X-RAY DIFFRACTION4G1 - 153
5X-RAY DIFFRACTION5I1 - 153
6X-RAY DIFFRACTION6K1 - 153
7X-RAY DIFFRACTION7M1 - 153
8X-RAY DIFFRACTION8O1 - 153
9X-RAY DIFFRACTION9Q1 - 153
10X-RAY DIFFRACTION10S1 - 153
11X-RAY DIFFRACTION11U1 - 153
12X-RAY DIFFRACTION12W2 - 153

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