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- PDB-3qqd: Human SOD1 H80R variant, P212121 crystal form -

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Basic information

Entry
Database: PDB / ID: 3qqd
TitleHuman SOD1 H80R variant, P212121 crystal form
Components(Superoxide dismutase [Cu-Zn]) x 2
KeywordsOXIDOREDUCTASE / HUMAN CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / DISEASE MUTATION / DISULFIDE BOND
Function / homology
Function and homology information


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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / 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 / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / glutathione metabolic process / axon cytoplasm / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / positive regulation of cytokine production / determination of adult lifespan / placenta development / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsSeetharaman, S.V. / Winkler, D.D. / Taylor, A.B. / Cao, X. / Whitson, L.J. / Doucette, P.A. / Valentine, J.S. / Schirf, V. / Demeler, B. / Carroll, M.C. ...Seetharaman, S.V. / Winkler, D.D. / Taylor, A.B. / Cao, X. / Whitson, L.J. / Doucette, P.A. / Valentine, J.S. / Schirf, V. / Demeler, B. / Carroll, M.C. / Culotta, V.C. / Hart, P.J.
CitationJournal: Biochemistry / Year: 2010
Title: Disrupted zinc-binding sites in structures of pathogenic SOD1 variants D124V and H80R.
Authors: Seetharaman, S.V. / Winkler, D.D. / Taylor, A.B. / Cao, X. / Whitson, L.J. / Doucette, P.A. / Valentine, J.S. / Schirf, V. / Demeler, B. / Carroll, M.C. / Culotta, V.C. / Hart, P.J.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionMar 9, 2011ID: 3H2R
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,1326
Polymers31,8092
Non-polymers3234
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-96 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.245, 58.427, 104.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 15920.646 Da / Num. of mol.: 1 / Mutation: YES
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: Protein Superoxide dismutase [Cu-Zn]


Mass: 15888.647 Da / Num. of mol.: 1 / Mutation: YES
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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.94 Å3/Da / Density % sol: 36.61 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 2.3 M AMMONIUM SULFATE, 0.1 M TRIS, TEMPERATURE 298K, pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.282 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 30227 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.064 / Net I/σ(I): 23.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.385 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1AZV

1azv


Resolution: 1.653→39.015 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 16.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 1533 5.07 %random
Rwork0.1445 ---
obs0.1466 30227 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8194 Å20 Å20 Å2
2--0.9662 Å20 Å2
3----0.5823 Å2
Refinement stepCycle: LAST / Resolution: 1.653→39.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 12 188 2023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051862
X-RAY DIFFRACTIONf_angle_d0.9132518
X-RAY DIFFRACTIONf_dihedral_angle_d10.365649
X-RAY DIFFRACTIONf_chiral_restr0.063287
X-RAY DIFFRACTIONf_plane_restr0.003332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6532-1.70650.27371130.22642500X-RAY DIFFRACTION97
1.7065-1.76750.21121280.15462583X-RAY DIFFRACTION99
1.7675-1.83830.19971290.12322585X-RAY DIFFRACTION100
1.8383-1.9220.18451370.09672572X-RAY DIFFRACTION100
1.922-2.02330.14091440.10042585X-RAY DIFFRACTION100
2.0233-2.15010.13871400.09962588X-RAY DIFFRACTION100
2.1501-2.3160.1821250.12192614X-RAY DIFFRACTION100
2.316-2.54910.19121450.14692614X-RAY DIFFRACTION100
2.5491-2.91780.18391440.16442628X-RAY DIFFRACTION100
2.9178-3.67570.1791570.1532655X-RAY DIFFRACTION100
3.6757-39.02570.19281710.16352770X-RAY DIFFRACTION100

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