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- PDB-6flh: Monomeric Human Cu,Zn Superoxide dismutase, SOD1 7+7, apo form -

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Basic information

Entry
Database: PDB / ID: 6flh
TitleMonomeric Human Cu,Zn Superoxide dismutase, SOD1 7+7, apo form
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1
Function / homology
Function and homology information


positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / action potential initiation / regulation of T cell differentiation in thymus / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / regulation of organ growth / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to superoxide ...positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / action potential initiation / regulation of T cell differentiation in thymus / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / regulation of organ growth / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to superoxide / anterograde axonal transport / protein phosphatase 2B binding / dense core granule / Oxidoreductases; Acting on a sulfur group of donors / regulation of GTPase activity / auditory receptor cell stereocilium organization / retina homeostasis / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / myeloid cell homeostasis / superoxide anion generation / muscle cell cellular homeostasis / superoxide metabolic process / response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / heart contraction / superoxide dismutase activity / cellular response to cadmium ion / regulation of multicellular organism growth / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / response to axon injury / ectopic germ cell programmed cell death / ovarian follicle development / neuronal action potential / embryo implantation / positive regulation of superoxide anion generation / axon cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / thymus development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / placenta development / positive regulation of phagocytosis / dendrite cytoplasm / response to amphetamine / determination of adult lifespan / positive regulation of cytokine production / regulation of mitochondrial membrane potential / glutathione metabolic process / response to hydrogen peroxide / sensory perception of sound / locomotory behavior / response to nutrient levels / negative regulation of inflammatory response / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / response to heat / protein-folding chaperone binding / gene expression / cytoplasmic vesicle / spermatogenesis / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / response to ethanol / positive regulation of MAPK cascade / lysosome / response to xenobiotic stimulus / positive regulation of apoptotic process / mitochondrial matrix / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / : / 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 / molecular replacement / Resolution: 1.79 Å
AuthorsWang, H. / Yang, F. / Logan, D. / Oliveberg, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2018
Title: The Cost of Long Catalytic Loops in Folding and Stability of the ALS-Associated Protein SOD1.
Authors: Yang, F. / Wang, H. / Logan, D.T. / Mu, X. / Danielsson, J. / Oliveberg, M.
History
DepositionJan 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Advisory / Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_validate_close_contact
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.3Jan 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

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0753
Polymers11,8871
Non-polymers1882
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-19 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.214, 83.214, 133.478
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-359-

HOH

31A-365-

HOH

41A-391-

HOH

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Components

#1: Protein Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 11887.126 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.6 and 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→63.41 Å / Num. obs: 16779 / % possible obs: 98.7 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Rrim(I) all: 0.088 / Net I/σ(I): 20.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.836.60.7828100.7180.3090.84480.6
8.96-63.417.70.0371600.9980.0140.0498.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
MOLREPphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BCZ

4bcz


Resolution: 1.79→63.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.919 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.089
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 863 5.1 %RANDOM
Rwork0.1698 ---
obs0.1712 15915 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 125.75 Å2 / Biso mean: 31.433 Å2 / Biso min: 12.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.79→63.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms837 0 11 94 942
Biso mean--35.71 41.98 -
Num. residues----118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.019891
X-RAY DIFFRACTIONr_bond_other_d0.0030.02825
X-RAY DIFFRACTIONr_angle_refined_deg2.3631.9481210
X-RAY DIFFRACTIONr_angle_other_deg1.1931921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66126.28635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50315141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.451152
X-RAY DIFFRACTIONr_chiral_restr0.1640.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02159
LS refinement shellResolution: 1.792→1.839 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 45 -
Rwork0.269 987 -
all-1032 -
obs--83.56 %

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