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- PDB-5j0c: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -

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Basic information

Entry
Database: PDB / ID: 5j0c
TitleMonomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, circular permutant P2/3
ComponentsSuperoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / 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 ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / 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 / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / 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 / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / 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
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
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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],Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)22,5552
Polymers22,5552
Non-polymers00
Water3,459192
1
A: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)11,2781
Polymers11,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)11,2781
Polymers11,2781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.310, 73.310, 68.680
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],Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 11277.669 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5 / Details: 0.1 M MIB buffer pH 5.0 25 % w/v PEG 1500 / PH range: 5

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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: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→24 Å / Num. obs: 27738 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.9
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.63

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Processing

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

4bcz


Resolution: 1.6→23.32 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.913 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.079
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 1384 5 %RANDOM
Rwork0.1436 ---
obs0.1458 26317 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.31 Å2 / Biso mean: 23.238 Å2 / Biso min: 8.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.13 Å20 Å2
2--0.13 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 1.6→23.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 0 192 1762
Biso mean---32.63 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191600
X-RAY DIFFRACTIONr_bond_other_d0.0010.021575
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9432161
X-RAY DIFFRACTIONr_angle_other_deg0.71633624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65825.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8315254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.883154
X-RAY DIFFRACTIONr_chiral_restr0.0680.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02332
X-RAY DIFFRACTIONr_mcbond_it2.7372.051907
X-RAY DIFFRACTIONr_mcbond_other2.7182.046906
X-RAY DIFFRACTIONr_mcangle_it3.4983.0761132
X-RAY DIFFRACTIONr_rigid_bond_restr3.06233175
X-RAY DIFFRACTIONr_sphericity_free34.805559
X-RAY DIFFRACTIONr_sphericity_bonded12.853287
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 87 -
Rwork0.173 1948 -
all-2035 -
obs--99.8 %

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