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- PDB-3h2q: Human SOD1 H80R variant, P21 crystal form -

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Basic information

Entry
Database: PDB / ID: 3h2q
TitleHuman SOD1 H80R variant, P21 crystal form
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / human cu / zn superoxide dismutase / antioxidant / metal-binding / copper / zinc / amyotrophic lateral sclerosis / disease mutation / Acetylation / Cytoplasm / Disulfide bond / Phosphoprotein / Ubl conjugation
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeetharaman, S.V. / Winkler, D.D. / Taylor, A.B. / Cao, X. / Whitson, L.J. / Doucette, P.A. / Valentine, J.S. / Carroll, M.C. / Culotta, V.C. / Hart, P.J.
CitationJournal: To be Published
Title: Structures of Pathogenic SOD1 Mutants H80R and D124V: Disrupted Zinc-binding and Compromised Post-translational Modification by the Copper Chaperone CCS
Authors: Seetharaman, S.V. / Winkler, D.D. / Taylor, A.B. / Cao, X. / Whitson, L.J. / Doucette, P.A. / Valentine, J.S. / Carroll, M.C. / Culotta, V.C. / Hart, P.J.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,03212
Polymers63,3864
Non-polymers6468
Water6,648369
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0166
Polymers31,6932
Non-polymers3234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-124 kcal/mol
Surface area13140 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0166
Polymers31,6932
Non-polymers3234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-122 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.240, 136.801, 56.364
Angle α, β, γ (deg.)90.00, 104.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 15846.607 Da / Num. of mol.: 4 / Mutation: H80R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351-HSOD / Production host: saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EGY118 / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.3 M AMMONIUM SULFATE, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 27, 2003 / 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
ReflectionResolution: 1.85→30 Å / Num. obs: 41506 / % possible obs: 94.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.99 Å2 / Rsym value: 0.09 / Net I/σ(I): 21.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 4141 / Rsym value: 0.531 / % possible all: 95.3

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Processing

Software
NameClassification
CrystalCleardata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZV

1azv


Resolution: 1.85→25.335 Å / SU ML: 0.22 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 2052 4.95 %RANDOM
Rwork0.1794 ---
obs0.1816 41462 94.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.547 Å2 / ksol: 0.424 e/Å3
Displacement parametersBiso mean: 25.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.9051 Å20 Å20.6144 Å2
2---4.6855 Å20 Å2
3----4.2416 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 24 369 4161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.04
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8930.24641200.19572605X-RAY DIFFRACTION94
1.893-1.94040.26821390.18522656X-RAY DIFFRACTION94
1.9404-1.99280.22461130.18392624X-RAY DIFFRACTION95
1.9928-2.05140.22461350.16492640X-RAY DIFFRACTION95
2.0514-2.11760.22421240.1652616X-RAY DIFFRACTION95
2.1176-2.19320.22471600.17312633X-RAY DIFFRACTION95
2.1932-2.2810.25081430.17172653X-RAY DIFFRACTION96
2.281-2.38470.23311300.17542653X-RAY DIFFRACTION95
2.3847-2.51040.2021460.18072697X-RAY DIFFRACTION97
2.5104-2.66750.2541360.19922730X-RAY DIFFRACTION98
2.6675-2.87320.26021470.20222700X-RAY DIFFRACTION98
2.8732-3.16180.25541560.19282750X-RAY DIFFRACTION98
3.1618-3.61820.20291140.16922158X-RAY DIFFRACTION78
3.6182-4.55430.18151340.14832495X-RAY DIFFRACTION89
4.5543-25.33730.18081550.172800X-RAY DIFFRACTION100

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