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- PDB-3hff: Monomeric human Cu,Zn Superoxide dismutase without Zn ligands -

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Basic information

Entry
Database: PDB / ID: 3hff
TitleMonomeric human Cu,Zn Superoxide dismutase without Zn ligands
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1 / MONOMERIC MUTANT / Amyotrophic lateral sclerosis / Antioxidant / Disease mutation / Disulfide bond / Metal-binding / Neurodegeneration / Phosphoprotein
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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSaraboji, K. / Nordlund, A. / Leinartait, L. / Oliveberg, M. / Logan, D.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Functional features cause misfolding of the ALS-provoking enzyme SOD1.
Authors: Nordlund, A. / Leinartaite, L. / Saraboji, K. / Aisenbrey, C. / Grobner, G. / Zetterstrom, P. / Danielsson, J. / Logan, D.T. / Oliveberg, M.
History
DepositionMay 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9636
Polymers15,6361
Non-polymers3275
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Superoxide dismutase [Cu-Zn]
hetero molecules

A: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,92712
Polymers31,2722
Non-polymers65410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1130 Å2
ΔGint-6 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.670, 36.670, 144.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe oligomeric state predicted by PISA is a putative dimer.

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Components

#1: Protein Superoxide dismutase [Cu-Zn] / CU/ZN SUPEROXIDE DISMUTASE


Mass: 15636.213 Da / Num. of mol.: 1 / Mutation: C6A, C111A, F50E, G51E, H63S, H71S, H80S, D83S
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 / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.79 Å3/Da / Density % sol: 31.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG 6000, 10% Jeffamine M-600 (pH 7.0), 0.1M Tris-HCl (pH 8.0), 0.1M ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.9083 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9083 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 5811 / Num. obs: 5811 / % possible obs: 93.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.35
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.17 / Num. unique all: 623 / % possible all: 82.7

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0044refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→17.13 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.876 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28087 559 9.6 %RANDOM
Rwork0.22363 ---
obs0.22914 5250 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→17.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 5 28 851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021828
X-RAY DIFFRACTIONr_bond_other_d0.0010.02529
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.951116
X-RAY DIFFRACTIONr_angle_other_deg1.74331310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8395112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.52726.2532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79815136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.184152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
X-RAY DIFFRACTIONr_mcbond_it0.6241.5556
X-RAY DIFFRACTIONr_mcbond_other0.1261.5246
X-RAY DIFFRACTIONr_mcangle_it1.1262880
X-RAY DIFFRACTIONr_scbond_it1.6983272
X-RAY DIFFRACTIONr_scangle_it2.8744.5236
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 32 -
Rwork0.306 329 -
obs--82.05 %
Refinement TLS params.Method: refined / Origin x: 15.1292 Å / Origin y: -15.984 Å / Origin z: 10.2232 Å
111213212223313233
T0.0363 Å2-0.0429 Å20.0156 Å2-0.0721 Å2-0.0026 Å2--0.0888 Å2
L2.2575 °2-0.1098 °20.5447 °2-3.2447 °2-1.4004 °2--5.6545 °2
S-0.0025 Å °-0.1628 Å °0.0625 Å °-0.0368 Å °-0.0899 Å °-0.1844 Å °-0.183 Å °0.2118 Å °0.0925 Å °

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