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- PDB-5j0f: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -

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Basic information

Entry
Database: PDB / ID: 5j0f
TitleMonomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, circular permutant P4/5
ComponentsSuperoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / 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 / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / 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: 1.25 Å
AuthorsWang, H. / Lang, L. / Logan, D. / Danielsson, J. / Oliveberg, M.
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Tricking a Protein To Swap Strands.
Authors: Wang, H. / Lang, L. / Logan, D.T. / Danielsson, J. / Oliveberg, M.
History
DepositionMar 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 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],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9827
Polymers22,5212
Non-polymers4605
Water4,738263
1
A: Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5374
Polymers11,2611
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4453
Polymers11,2611
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.720, 71.720, 69.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 11260.579 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.17 M ammonium sulfate, 25.5 % w/v PEG 4K, 15 % v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→46.36 Å / Num. obs: 56396 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 29.2
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.563

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bcz

4bcz


Resolution: 1.25→46.36 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.084 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.041
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 2848 5.1 %RANDOM
Rwork0.1293 ---
obs0.1313 53233 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 205.76 Å2 / Biso mean: 20.982 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å20 Å2
2--0.08 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.25→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 30 263 1879
Biso mean--40.69 39.31 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191631
X-RAY DIFFRACTIONr_bond_other_d0.0060.021604
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.9562195
X-RAY DIFFRACTIONr_angle_other_deg0.90533690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9595226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.01725.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73215252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.32154
X-RAY DIFFRACTIONr_chiral_restr0.1470.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_mcbond_it4.5481.71910
X-RAY DIFFRACTIONr_mcbond_other4.5441.708909
X-RAY DIFFRACTIONr_mcangle_it5.4632.5771134
X-RAY DIFFRACTIONr_rigid_bond_restr5.66333235
X-RAY DIFFRACTIONr_sphericity_free53.62569
X-RAY DIFFRACTIONr_sphericity_bonded24.16853414
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 237 -
Rwork0.197 3955 -
all-4192 -
obs--100 %

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