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- PDB-6dtk: Heterodimers of FALS mutant SOD enzyme -

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Basic information

Entry
Database: PDB / ID: 6dtk
TitleHeterodimers of FALS mutant SOD enzyme
ComponentsSuperoxide dismutase C111S/D83S-C111S HETERODIMER
KeywordsOXIDOREDUCTASE / Copper/Zinc superoxide dismutase Cu / Zn-SOD1 / metal binding protein / FALS Zn-deficient 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
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / MALONATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStreltsov, V.A. / Nuttall, S.D. / Ganio, K.E. / Roberts, B.
CitationJournal: To Be Published
Title: Structural characterization of heterodimers of FALS mutant SOD enzyme
Authors: Streltsov, V.A. / Nuttall, S.D. / Ganio, K.E. / Roberts, B.
History
DepositionJun 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase C111S/D83S-C111S HETERODIMER
C: Superoxide dismutase C111S/D83S-C111S HETERODIMER
E: Superoxide dismutase C111S/D83S-C111S HETERODIMER
G: Superoxide dismutase C111S/D83S-C111S HETERODIMER
I: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,01726
Polymers163,6265
Non-polymers1,39221
Water24,4281356
1
A: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9835
Polymers32,7251
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9835
Polymers32,7251
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0856
Polymers32,7251
Non-polymers3605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9835
Polymers32,7251
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Superoxide dismutase C111S/D83S-C111S HETERODIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9835
Polymers32,7251
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.699, 201.671, 143.834
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
11A-701-

HOH

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Components

#1: Protein
Superoxide dismutase C111S/D83S-C111S HETERODIMER / Superoxide dismutase 1 / hSod1


Mass: 32725.129 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1356 / Source method: isolated from a natural source / Formula: H2O
Compound detailsChimeric construct: mutated and WT protein chains are linked via linker and form a heterodimer. Due ...Chimeric construct: mutated and WT protein chains are linked via linker and form a heterodimer. Due to almost two fold symmetry of the heterodimer and structural similarity to the WT protein (or possible admixture of homodimers formed due to broken linker), the crystal electron density shows an average picture with fractional mixed DS populations on positions 83 and 252.
Has protein modificationY

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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: 3.65 Å3/Da / Density % sol: 66.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2-3 M Ammonium sulfate or Sodium malonate / PH range: 4.5-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2013 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→47.57 Å / Num. obs: 158995 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 14.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.25
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.47 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FUN

1fun


Resolution: 2→47.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.021 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 7971 5 %RANDOM
Rwork0.156 ---
obs0.158 150990 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2--0.4 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11297 0 27 1356 12680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01511661
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710387
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.64515651
X-RAY DIFFRACTIONr_angle_other_deg1.1931.6624408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.1815.4171629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5324.494514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.406151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5861539
X-RAY DIFFRACTIONr_chiral_restr0.1660.21477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214484
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022051
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.833.5986289
X-RAY DIFFRACTIONr_mcbond_other2.8293.5986288
X-RAY DIFFRACTIONr_mcangle_it4.1875.3747859
X-RAY DIFFRACTIONr_mcangle_other4.1885.3747860
X-RAY DIFFRACTIONr_scbond_it3.9464.0745372
X-RAY DIFFRACTIONr_scbond_other3.9464.0745370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2435.8827791
X-RAY DIFFRACTIONr_long_range_B_refined8.99746.04112809
X-RAY DIFFRACTIONr_long_range_B_other8.81745.0112362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 576 -
Rwork0.225 10937 -
obs--98.88 %

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