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- PDB-1azv: FAMILIAL ALS MUTANT G37R CUZNSOD (HUMAN) -

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Basic information

Entry
Database: PDB / ID: 1azv
TitleFAMILIAL ALS MUTANT G37R CUZNSOD (HUMAN)
ComponentsCOPPER/ZINC SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / SUPEROXIDE ACCEPTOR / FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS MUTANT
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / 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 ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / 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 / peripheral nervous system myelin maintenance / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / 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
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHart, P.J. / Liu, H. / Pellegrini, M. / Nersissian, A.M. / Gralla, E.B. / Valentine, J.S. / Eisenberg, D.
CitationJournal: Protein Sci. / Year: 1998
Title: Subunit asymmetry in the three-dimensional structure of a human CuZnSOD mutant found in familial amyotrophic lateral sclerosis.
Authors: Hart, P.J. / Liu, H. / Pellegrini, M. / Nersissian, A.M. / Gralla, E.B. / Valentine, J.S. / Eisenberg, D.
History
DepositionNov 21, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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.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 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COPPER/ZINC SUPEROXIDE DISMUTASE
B: COPPER/ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1136
Polymers31,8552
Non-polymers2584
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-25 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.200, 67.200, 83.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein COPPER/ZINC SUPEROXIDE DISMUTASE / CUZNSOD


Mass: 15927.703 Da / Num. of mol.: 2 / Mutation: G37R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: SOD1 / Cellular location (production host): CYTOPLASM / Gene (production host): YEAST CUZNSOD PROMOTER / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG118 / References: UniProt: P00441, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growpH: 5.5
Details: 20 MG/ML PROTEIN IN 10MM ACETATE PH 5.5 MIXED WITH PRECIPITATING SOLUTION OF 100 MM ACETATE PH 4.6, 2.0 M AMMONIUM SULFATE
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
25 mMacetate11
350 mMsodium acetate11
41.0 Mammonium sulfate11
5100 mMsodium acetate12
62.0 Mammonium sulfate12

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 29129 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.065 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.383 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 101819 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.383

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SPD

1spd


Resolution: 1.9→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2889 9.9 %RANDOM
Rwork0.202 ---
obs0.202 28975 99.3 %-
Displacement parametersBiso mean: 29 Å2
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 4 176 2414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.368 343 9.4 %
Rwork0.344 3265 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47

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