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- PDB-5ucx: Structure of S78C Human Peroxiredoxin 3 as three stacked rings -

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Basic information

Entry
Database: PDB / ID: 5ucx
TitleStructure of S78C Human Peroxiredoxin 3 as three stacked rings
ComponentsThioredoxin-dependent peroxide reductase, mitochondrial
KeywordsOXIDOREDUCTASE / chaperone / stacked ring / peroxiredoxin 3 / typical 2-Cys / peroxidase
Function / homology
Function and homology information


peptidyl-cysteine oxidation / alkyl hydroperoxide reductase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / negative regulation of kinase activity / Detoxification of Reactive Oxygen Species / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cell redox homeostasis ...peptidyl-cysteine oxidation / alkyl hydroperoxide reductase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / negative regulation of kinase activity / Detoxification of Reactive Oxygen Species / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cell redox homeostasis / regulation of mitochondrial membrane potential / mitochondrion organization / hydrogen peroxide catabolic process / response to hydrogen peroxide / cellular response to reactive oxygen species / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / response to oxidative stress / response to lipopolysaccharide / early endosome / mitochondrial matrix / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-dependent peroxide reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsYewdall, N.A. / Gerrard, J.A. / Goldstone, G.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Army Research Office United States
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Quaternary structure influences the peroxidase activity of peroxiredoxin 3.
Authors: Yewdall, N.A. / Peskin, A.V. / Hampton, M.B. / Goldstone, D.C. / Pearce, F.G. / Gerrard, J.A.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.4Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-dependent peroxide reductase, mitochondrial
B: Thioredoxin-dependent peroxide reductase, mitochondrial
C: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
E: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)199,8929
Polymers199,8929
Non-polymers00
Water1,04558
1
A: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial

A: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial

A: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial

A: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)266,52312
Polymers266,52312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area32920 Å2
ΔGint-245 kcal/mol
Surface area81690 Å2
MethodPISA
2
C: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial

C: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial

E: Thioredoxin-dependent peroxide reductase, mitochondrial

E: Thioredoxin-dependent peroxide reductase, mitochondrial

B: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial

B: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)266,52312
Polymers266,52312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_558x,-y,-z+31
crystal symmetry operation5_445x-1/2,y-1/2,z+1/21
crystal symmetry operation8_457x-1/2,-y+1/2,-z+5/21
crystal symmetry operation6_455-x-1/2,-y+1/2,z+1/21
crystal symmetry operation7_447-x-1/2,y-1/2,-z+5/21
Buried area32740 Å2
ΔGint-250 kcal/mol
Surface area82220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.449, 167.590, 221.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Thioredoxin-dependent peroxide reductase, mitochondrial / Antioxidant protein 1 / AOP-1 / HBC189 / Peroxiredoxin III / Prx-III / Peroxiredoxin-3 / Protein MER5 homolog


Mass: 22210.227 Da / Num. of mol.: 9 / Mutation: S78C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX3, AOP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30048, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.1 Å3/Da / Density % sol: 60.3 % / Description: Nice Rod!
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 12.5% PEG1000, 12.5% PEG3350. 12.5% MPD, 0.02 M alcohol additives at pH 8.7 (Fine screen derived from Gorrec, 2009)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→48.92 Å / Num. obs: 96714 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.266 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.445.61.4620.379199.2
2.4-48.926.40.2660.98199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata collection
Aimless0.3.11data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.92 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.059 / SU ML: 0.176 / SU R Cruickshank DPI: 0.2875 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.215
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 4717 4.9 %RANDOM
Rwork0.1939 ---
obs0.1956 91953 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.25 Å2 / Biso mean: 24.167 Å2 / Biso min: 9.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2--1.07 Å20 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 2.4→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13640 0 0 58 13698
Biso mean---18.9 -
Num. residues----1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914009
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212755
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.95119101
X-RAY DIFFRACTIONr_angle_other_deg0.957329630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27551746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4924.475619
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.393152160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8011545
X-RAY DIFFRACTIONr_chiral_restr0.080.22160
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115652
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022853
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 322 -
Rwork0.299 6753 -
all-7075 -
obs--99.1 %

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