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- PDB-3gtt: Mouse SOD1 -

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Basic information

Entry
Database: PDB / ID: 3gtt
TitleMouse SOD1
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / MOUSE CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / Disulfide bond / Phosphoprotein
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / dense core granule / Platelet degranulation / 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 ...Detoxification of Reactive Oxygen Species / dense core granule / Platelet degranulation / 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 / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / superoxide anion generation / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / response to copper ion / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / 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 / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / response to reactive oxygen species / response to nutrient levels / positive regulation of superoxide anion generation / locomotory behavior / regulation of mitochondrial membrane potential / secretory granule / 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 / myelin sheath / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / response to oxidative stress / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / lysosome / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / negative regulation of apoptotic process / enzyme binding / protein-containing complex / mitochondrion / extracellular space / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeetharaman, S.V. / Taylor, A.B. / Hart, P.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2010
Title: Structures of mouse SOD1 and human/mouse SOD1 chimeras.
Authors: Seetharaman, S.V. / Taylor, A.B. / Holloway, S. / Hart, P.J.
History
DepositionMar 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,39912
Polymers95,0076
Non-polymers3926
Water13,007722
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8004
Polymers31,6692
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-9 kcal/mol
Surface area13720 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8004
Polymers31,6692
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area13730 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8004
Polymers31,6692
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.454, 194.495, 149.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-653-

HOH

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15834.496 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sod1 / Plasmid: pKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08228, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 4.31 Å3/Da / Density % sol: 71.47 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 0.1 M Tris, 30% PEG 1000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 18, 2008 / Details: MIRRORS
RadiationMonochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: 1/2*h+1/2*k,3/2*h-1/2*k,-l / Fraction: 0.144
ReflectionResolution: 2.4→30 Å / Num. obs: 64203 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 29.6 Å2 / Rsym value: 0.105 / Net I/σ(I): 11.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.463 / % possible all: 100

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Processing

Software
NameClassification
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VR7

2vr7


Resolution: 2.4→23.76 Å / Isotropic thermal model: isotropic / σ(F): 1.33
RfactorNum. reflection% reflection
Rfree0.197 3210 5 %
Rwork0.158 --
obs0.16 64174 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.16 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.8681 Å20 Å20 Å2
2---6.8886 Å20 Å2
3---6.454 Å2
Refinement stepCycle: LAST / Resolution: 2.4→23.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 0 6 722 7382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066762
X-RAY DIFFRACTIONf_angle_d1.0769114
X-RAY DIFFRACTIONf_dihedral_angle_d18.4692436
X-RAY DIFFRACTIONf_chiral_restr0.068990
X-RAY DIFFRACTIONf_plane_restr0.0041248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4142-2.45520.28362140.22752871X-RAY DIFFRACTION93
2.4552-2.4990.23741070.22193011X-RAY DIFFRACTION97
2.499-2.54620.25462140.21542805X-RAY DIFFRACTION93
2.5462-2.59720.2221070.21492984X-RAY DIFFRACTION97
2.5972-2.65250.25482140.20612839X-RAY DIFFRACTION93
2.6525-2.71280.25731070.20272992X-RAY DIFFRACTION97
2.7128-2.77910.24992140.20142869X-RAY DIFFRACTION93
2.7791-2.85230.2361070.19872980X-RAY DIFFRACTION97
2.8523-2.93390.24721070.19542997X-RAY DIFFRACTION96
2.9339-3.02570.21782140.17572896X-RAY DIFFRACTION93
3.0257-3.13020.21711070.16712979X-RAY DIFFRACTION97
3.1302-3.25090.20262140.15732852X-RAY DIFFRACTION93
3.2509-3.39250.17921070.14523013X-RAY DIFFRACTION97
3.3925-3.56270.17972140.14582880X-RAY DIFFRACTION93
3.5627-3.7730.16671070.13243016X-RAY DIFFRACTION97
3.773-4.04390.15212140.12392908X-RAY DIFFRACTION93
4.0439-4.41440.14411070.11273030X-RAY DIFFRACTION97
4.4144-4.97360.17512140.11672921X-RAY DIFFRACTION93
4.9736-5.99930.19851070.14813071X-RAY DIFFRACTION97
5.9993-9.58740.17862140.17033014X-RAY DIFFRACTION93

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