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

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Basic information

Entry
Database: PDB / ID: 4dsr
TitleCrystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in reduced 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 / cytosol / cytoplasm
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: 2.91 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

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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
Water19811
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 area1180 Å2
ΔGint-13 kcal/mol
Surface area15660 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 area1140 Å2
ΔGint-13 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.463, 154.463, 90.966
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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.: 11 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% polyethylene glycol 3350, 0.2M ammonium sulfate, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.91→50 Å / Num. all: 16465 / Num. obs: 16465 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 70.2 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 7.68
Reflection shellResolution: 2.91→3.01 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.991 / Num. unique all: 1642 / Rsym value: 0.369 / % possible all: 91.5

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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: 2.91→44.2 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27423 835 5.2 %RANDOM
Rwork0.23872 ---
obs0.24051 15358 91.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å2-0.75 Å20 Å2
2---1.51 Å20 Å2
3---2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.91→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5328 0 0 11 5339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225452
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9427432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.18225.926216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5915884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.112154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214080
X-RAY DIFFRACTIONr_mcbond_it0.3591.53468
X-RAY DIFFRACTIONr_mcangle_it0.68125636
X-RAY DIFFRACTIONr_scbond_it0.99531984
X-RAY DIFFRACTIONr_scangle_it1.6494.51796
LS refinement shellResolution: 2.91→2.986 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 67 -
Rwork0.306 1144 -
obs--93.01 %

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