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- PDB-5j0g: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -

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Basic information

Entry
Database: PDB / ID: 5j0g
TitleMonomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, circular permutant P7/8
ComponentsOXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1
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 / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / 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 / 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 / cellular response to ATP / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / cellular response to cadmium ion / 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 / regulation of mitochondrial membrane potential / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / placenta development / response to amphetamine / thymus development / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / mitochondrial intermembrane space / small GTPase binding / 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: 2.5 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: OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
B: OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)22,3792
Polymers22,3792
Non-polymers00
Water43224
1
A: OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)11,1891
Polymers11,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)11,1891
Polymers11,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.140, 74.140, 59.420
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 OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 11189.499 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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium hydrogen citrate, 20 % w/v PEG 3350

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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: 2.5→37.1 Å / Num. obs: 6519 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.61 Å / Rmerge(I) obs: 0.661

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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: 2.5→37.1 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 25.382 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.304
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 304 4.7 %RANDOM
Rwork0.1818 ---
obs0.1843 6195 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.19 Å2 / Biso mean: 48.959 Å2 / Biso min: 16.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0.67 Å2-0 Å2
2---0.67 Å2-0 Å2
3---2.19 Å2
Refinement stepCycle: final / Resolution: 2.5→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 0 24 1600
Biso mean---35.26 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191596
X-RAY DIFFRACTIONr_bond_other_d0.0010.021564
X-RAY DIFFRACTIONr_angle_refined_deg0.8811.9452156
X-RAY DIFFRACTIONr_angle_other_deg0.59833598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03525.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18415252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.581154
X-RAY DIFFRACTIONr_chiral_restr0.0570.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
X-RAY DIFFRACTIONr_mcbond_it2.8993.791902
X-RAY DIFFRACTIONr_mcbond_other2.8973.785901
X-RAY DIFFRACTIONr_mcangle_it3.85.6561124
X-RAY DIFFRACTIONr_rigid_bond_restr1.27133160
X-RAY DIFFRACTIONr_sphericity_free28.881516
X-RAY DIFFRACTIONr_sphericity_bonded19.77553148
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 28 -
Rwork0.279 449 -
all-477 -
obs--100 %
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)
10.08650.0223-0.0660.0091-0.00870.0869-0.0290.01410.0349-0.01080.00370.0294-0.01070.02490.02540.1269-0.0085-0.020.12580.01580.1404-5.076426.69780.0766
20.385-0.0890.14950.022-0.03470.0592-0.0441-0.04260.09090.00510.0132-0.0324-0.0064-0.01830.03090.12430.0081-0.00340.1224-0.01280.13341.225726.994322.4106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 113

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