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- PDB-3hy2: Crystal Structure of Sulfiredoxin in Complex with Peroxiredoxin I... -

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Basic information

Entry
Database: PDB / ID: 3hy2
TitleCrystal Structure of Sulfiredoxin in Complex with Peroxiredoxin I and ATP:Mg2+
Components
  • Peroxiredoxin-1
  • Sulfiredoxin-1
KeywordsOXIDOREDUCTASE / protein-protein Complex / redox biology / protein repair / sulfur chemistry / Antioxidant / Disulfide bond / Peroxidase / Phosphoprotein / Redox-active center / ATP-binding / Magnesium / Nucleotide-binding
Function / homology
Function and homology information


sulfiredoxin / oxidoreductase activity, acting on a sulfur group of donors / sulfiredoxin activity / leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell mediated cytotoxicity / natural killer cell activation / erythrocyte homeostasis ...sulfiredoxin / oxidoreductase activity, acting on a sulfur group of donors / sulfiredoxin activity / leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell mediated cytotoxicity / natural killer cell activation / erythrocyte homeostasis / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of stress-activated MAPK cascade / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / removal of superoxide radicals / canonical NF-kappaB signal transduction / peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / skeletal system development / TP53 Regulates Metabolic Genes / melanosome / cellular response to oxidative stress / fibroblast proliferation / response to oxidative stress / cell population proliferation / cadherin binding / endoplasmic reticulum membrane / extracellular space / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sulfiredoxin / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin ...Sulfiredoxin / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Peroxiredoxin-1 / Sulfiredoxin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJonsson, T.J. / Johnson, L.C. / Lowther, W.T.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Protein Engineering of the Quaternary Sulfiredoxin-Peroxiredoxin Enzyme-Substrate Complex Reveals the Molecular Basis for Cysteine Sulfinic Acid Phosphorylation
Authors: Jonsson, T.J. / Johnson, L.C. / Lowther, W.T.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Oct 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_asym_id / _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.ptnr3_auth_asym_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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxiredoxin-1
B: Peroxiredoxin-1
X: Sulfiredoxin-1
Y: Sulfiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1728
Polymers70,1094
Non-polymers1,0634
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-78 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.330, 92.410, 131.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that the biological unit of peroxiredoxin molecule is a decamer i.e. five dimers that form a ring or donut-like structure. This structure, however, is an engineered dimer.

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Components

#1: Protein Peroxiredoxin-1 / / Thioredoxin peroxidase 2 / Thioredoxin-dependent peroxide reductase 2 / Proliferation-associated ...Thioredoxin peroxidase 2 / Thioredoxin-dependent peroxide reductase 2 / Proliferation-associated gene protein / PAG / Natural killer cell-enhancing factor A / NKEF-A


Mass: 23063.066 Da / Num. of mol.: 2 / Mutation: C52D, C71S, C83E, A86E, C173S, K185C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX1, PAGA, PAGB, TDPX2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06830, peroxiredoxin
#2: Protein Sulfiredoxin-1 /


Mass: 11991.659 Da / Num. of mol.: 2 / Fragment: UNP residues 32 to 137 / Mutation: N43C, C99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf139, SRX, SRXN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYN0, sulfiredoxin
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.6
Details: 7-9.5% PEG 6000, 100 mM HEPES pH 7.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 11, 2008
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 41701 / % possible obs: 99.9 % / Observed criterion σ(I): 5.3
Reflection shellResolution: 2.1→2.18 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalClear(MSC/RIGAKU)data collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.38 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.544 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(I): 5.3 / ESU R: 0.235 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27282 2090 5 %RANDOM
Rwork0.22401 ---
obs0.22641 39439 99.68 %-
all-41661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.599 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4450 0 64 321 4835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224634
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9876321
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43124.229201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21715735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2171524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.22006
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23120
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8831.52930
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43924636
X-RAY DIFFRACTIONr_scbond_it2.19631944
X-RAY DIFFRACTIONr_scangle_it3.374.51685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 167 -
Rwork0.242 2812 -
obs--99.2 %

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