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- PDB-4dsq: Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevi... -

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Basic information

Entry
Database: PDB / ID: 4dsq
TitleCrystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in oxidized form
ComponentsPeroxiredoxin type-2
KeywordsOXIDOREDUCTASE / PEROXIREDOXIN / Peroxidase / Thioredoxin-like Fold / Alkyl hydroperoxide reductase
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / response to metal ion / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion ...TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / response to metal ion / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLian, F.M. / Yu, J. / Ma, X.X. / Yu, X.J. / Chen, Y. / Zhou, C.Z.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Snapshots of Yeast Alkyl Hydroperoxide Reductase Ahp1 Peroxiredoxin Reveal a Novel Two-cysteine Mechanism of Electron Transfer to Eliminate Reactive Oxygen Species
Authors: Lian, F.M. / Yu, J. / Ma, X.X. / Yu, X.J. / Chen, Y. / Zhou, C.Z.
History
DepositionFeb 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin type-2
B: Peroxiredoxin type-2
C: Peroxiredoxin type-2
D: Peroxiredoxin type-2


Theoretical massNumber of molelcules
Total (without water)80,5994
Polymers80,5994
Non-polymers00
Water3,315184
1
A: Peroxiredoxin type-2
B: Peroxiredoxin type-2


Theoretical massNumber of molelcules
Total (without water)40,2992
Polymers40,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-16 kcal/mol
Surface area15260 Å2
MethodPISA
2
C: Peroxiredoxin type-2
D: Peroxiredoxin type-2


Theoretical massNumber of molelcules
Total (without water)40,2992
Polymers40,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-16 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.978, 130.624, 67.678
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peroxiredoxin type-2 / AHPC1 / Cytoplasmic thiol peroxidase 3 / cTPx 3 / Peroxiredoxin type II / Peroxisomal alkyl ...AHPC1 / Cytoplasmic thiol peroxidase 3 / cTPx 3 / Peroxiredoxin type II / Peroxisomal alkyl hydroperoxide reductase / TPx type II / Thiol-specific antioxidant II / TSA II / Thioredoxin peroxidase type II / Thioredoxin reductase type II


Mass: 20149.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: AHP1, L2916, L9354.5, YLR109W / Plasmid: pET28a-derived / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P38013, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% polyethylene glycol monomethyl ether 2000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 25277 / Num. obs: 25277 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.174 / Rsym value: 0.174 / Net I/σ(I): 4.718
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.028 / Num. unique all: 1263 / Rsym value: 0.442 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TP9

1tp9


Resolution: 2.4→46.3 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / ESU R: 1.002 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27096 1272 5 %RANDOM
Rwork0.23612 ---
obs0.23789 23926 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.198 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å21.64 Å2
2---1.29 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5328 0 0 184 5512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9427440
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.07825.926216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58215884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.506154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1081.53468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7925636
X-RAY DIFFRACTIONr_scbond_it1.90631988
X-RAY DIFFRACTIONr_scangle_it3.3384.51804
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 80 -
Rwork0.256 1560 -
obs--85.33 %

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