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- PDB-3gtv: Human-mouse SOD1 chimera -

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Basic information

Entry
Database: PDB / ID: 3gtv
TitleHuman-mouse SOD1 chimera
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / human / MOUSE CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / Disease mutation / 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 / 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 ...Detoxification of Reactive Oxygen Species / dense core granule / Platelet degranulation / action potential initiation / neurofilament cytoskeleton organization / 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 / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of protein kinase activity / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / response to copper ion / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / superoxide dismutase / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / transmission of nerve impulse / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / 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 / response to nutrient levels / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / secretory granule / positive regulation of cytokine production / locomotory behavior / response to reactive oxygen species / determination of adult lifespan / sensory perception of sound / response to hydrogen peroxide / placenta development / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / Platelet degranulation / peroxisome / myelin sheath / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / response to oxidative stress / positive regulation of MAPK cascade / lysosome / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / negative regulation of apoptotic process / apoptotic process / enzyme binding / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / 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 / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn] / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 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]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,72524
Polymers190,94112
Non-polymers78512
Water32,5711808
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9544
Polymers31,8232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-12 kcal/mol
Surface area13950 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9544
Polymers31,8232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-12 kcal/mol
Surface area13890 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9544
Polymers31,8232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-12 kcal/mol
Surface area14010 Å2
MethodPISA
4
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9544
Polymers31,8232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-12 kcal/mol
Surface area13910 Å2
MethodPISA
5
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9544
Polymers31,8232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-12 kcal/mol
Surface area14030 Å2
MethodPISA
6
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9544
Polymers31,8232
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-11 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.625, 144.007, 112.613
Angle α, β, γ (deg.)90.00, 119.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15911.709 Da / Num. of mol.: 12
Fragment: residues 2-81 from human protein, residues 82-154 from mouse protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: SOD1 / Plasmid: pKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00441, UniProt: P08228, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1808 / 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: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.1 m HEPES, 25% PEG 8000, pH 7.5, 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: Dec 12, 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: l,-k,h / Fraction: 0.124
ReflectionResolution: 2.198→50 Å / Num. obs: 148445 / % possible obs: 94 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.7 Å2 / Rsym value: 0.111 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.476 / % possible all: 90

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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: 2.2→40.35 Å / Isotropic thermal model: isotropic / σ(F): 1.38
RfactorNum. reflection% reflection
Rfree0.231 7885 5.31 %
Rwork0.184 --
obs0.186 148404 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.2 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--9.1982 Å20 Å21.072 Å2
2--9.9521 Å20 Å2
3----2.3296 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13392 0 12 1808 15212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813614
X-RAY DIFFRACTIONf_angle_d1.17118334
X-RAY DIFFRACTIONf_dihedral_angle_d18.2154948
X-RAY DIFFRACTIONf_chiral_restr0.0771993
X-RAY DIFFRACTIONf_plane_restr0.0042486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2106-2.24810.29424980.25516335X-RAY DIFFRACTION84
2.2481-2.28830.2952490.25086677X-RAY DIFFRACTION87
2.2883-2.33160.29664980.25346360X-RAY DIFFRACTION84
2.3316-2.37830.27152490.24316666X-RAY DIFFRACTION88
2.3783-2.42890.29572490.24126677X-RAY DIFFRACTION88
2.4289-2.48420.29454980.23586402X-RAY DIFFRACTION84
2.4842-2.54490.28732490.23456671X-RAY DIFFRACTION87
2.5449-2.6120.29514980.23596478X-RAY DIFFRACTION84
2.612-2.68680.26582490.22426710X-RAY DIFFRACTION88
2.6868-2.7710.29462490.21596792X-RAY DIFFRACTION89
2.771-2.86680.27134980.21186701X-RAY DIFFRACTION88
2.8668-2.97740.28492490.20297043X-RAY DIFFRACTION92
2.9774-3.10730.24274980.18286892X-RAY DIFFRACTION90
3.1073-3.26340.20622490.16777146X-RAY DIFFRACTION94
3.2634-3.45650.21064980.15646917X-RAY DIFFRACTION91
3.4565-3.70520.20422490.157195X-RAY DIFFRACTION94
3.7052-4.04560.18774980.14427053X-RAY DIFFRACTION91
4.0456-4.56010.19232490.12987260X-RAY DIFFRACTION95
4.5601-5.50650.18614980.14867077X-RAY DIFFRACTION92
5.5065-8.87090.19574980.19167190X-RAY DIFFRACTION93

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