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- PDB-2vr7: Crystal Structure of G85R ALS mutant of Human Cu,Zn Superoxide Di... -

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Basic information

Entry
Database: PDB / ID: 2vr7
TitleCrystal Structure of G85R ALS mutant of Human Cu,Zn Superoxide Dismutase (CuZnSOD) at 1.58 A resolution
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE / ZINC / COPPER / HUMAN CU / CYTOPLASM / ACETYLATION / UBL CONJUGATION / DISEASE MUTATION / ZN SUPEROXIDE DISMUTASE / AMYOTROPHIC LATERAL SCLEROSIS / ANTIOXIDANT / METAL-BINDING
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / 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 / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / cellular response to ATP / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / cellular response to cadmium ion / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / placenta development / response to amphetamine / thymus development / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / 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 / THIOCYANATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsAntonyuk, S. / Cao, X. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Tiwari, A. / Hayward, L.J. ...Antonyuk, S. / Cao, X. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Tiwari, A. / Hayward, L.J. / Padua, S. / Cohlberg, J.A. / Selverstone Valentine, J. / Hasnain, S.S. / Hart, P.J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of the G85R Variant of Sod1 in Familial Amyotrophic Lateral Sclerosis.
Authors: Cao, X. / Antonyuk, S. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Valentine, J.S. / Tiwari, A. / Hayward, L.J. / Padua, S. / ...Authors: Cao, X. / Antonyuk, S. / Seetharaman, S.V. / Whitson, L.J. / Taylor, A.B. / Holloway, S.P. / Strange, R.W. / Doucette, P.A. / Valentine, J.S. / Tiwari, A. / Hayward, L.J. / Padua, S. / Cohlberg, J.A. / Hasnain, S.S. / Hart, P.J.
History
DepositionMar 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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.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 / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE [CU-ZN]
F: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,85116
Polymers31,9072
Non-polymers94414
Water11,241624
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-15.6 kcal/mol
Surface area17460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)36.768, 56.435, 75.028
Angle α, β, γ (deg.)90.00, 102.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AF

#1: Protein SUPEROXIDE DISMUTASE [CU-ZN]


Mass: 15953.741 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-154 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 5 types, 638 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


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.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 86 TO ARG ENGINEERED RESIDUE IN CHAIN F, GLY 86 TO ARG
Has protein modificationY
Sequence detailsG85R MUTANT

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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: 2.4 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7 / Details: 20% PEG3350, 0.2M SODIUM THIOCYANATE, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.48
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 25, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. obs: 38696 / % possible obs: 93.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 8.2 / % possible all: 73.5

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9S

2c9s


Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.158 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1947 5 %RANDOM
Rwork0.135 ---
obs0.137 36731 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.01 Å2
2---0.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 30 624 2894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212289
X-RAY DIFFRACTIONr_bond_other_d0.0020.022007
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.943088
X-RAY DIFFRACTIONr_angle_other_deg1.18634694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15115368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8381510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_nbd_refined0.2340.2474
X-RAY DIFFRACTIONr_nbd_other0.1870.22119
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21438
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5950.272
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5350.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0241.51509
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77722394
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6543780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1264.5693
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.193 90
Rwork0.145 1944

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