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

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Basic information

Entry
Database: PDB / ID: 4dss
TitleCrystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in complex with thioredoxin Trx2
Components
  • Peroxiredoxin type-2
  • Thioredoxin-2
KeywordsOXIDOREDUCTASE/TRANSPORT PROTEIN / Electron Transport / OXIDOREDUCTASE / PEROXIREDOXIN / Thioredoxin-2 / Thioredoxin Fold / Thioredoxin-like Fold / Alkyl hydroperoxide reductase / OXIDOREDUCTASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


membrane fusion priming complex / protein deglutathionylation / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / sulfate assimilation / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species ...membrane fusion priming complex / protein deglutathionylation / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / sulfate assimilation / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / Oxidative Stress Induced Senescence / response to metal ion / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / glutathione metabolic process / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / protein transport / cellular response to oxidative stress / Golgi membrane / mitochondrion / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-2 / Peroxiredoxin AHP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Jul 4, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.3Nov 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: Thioredoxin-2


Theoretical massNumber of molelcules
Total (without water)31,3312
Polymers31,3312
Non-polymers00
Water1,40578
1
A: Peroxiredoxin type-2
B: Thioredoxin-2

A: Peroxiredoxin type-2
B: Thioredoxin-2


Theoretical massNumber of molelcules
Total (without water)62,6634
Polymers62,6634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3480 Å2
ΔGint-36 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.703, 133.415, 78.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

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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: 19116.535 Da / Num. of mol.: 1 / Mutation: C62S
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: pET29a-derived / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P38013, peroxiredoxin
#2: Protein Thioredoxin-2 / Thioredoxin II / TR-II / Thioredoxin-1


Mass: 12214.898 Da / Num. of mol.: 1 / Mutation: C34S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: G7746, TRX1, TRX2, YGR209C / Plasmid: pET28a-derived / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P22803
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% polyethylene glycol 400, 0.2M Calcium chloride, 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: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17691 / Num. obs: 17691 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 12.76
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 4.276 / Num. unique all: 1754 / Rsym value: 0.339 / % possible all: 100

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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 1TP9,2FA4

1tp9

2fa4


Resolution: 2.1→26 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25889 875 5.1 %RANDOM
Rwork0.21936 ---
obs0.22134 16303 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.669 Å2
Baniso -1Baniso -2Baniso -3
1--3.06 Å20 Å20 Å2
2---0.98 Å20 Å2
3---4.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 0 78 2195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222162
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.952940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46125.95284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6515358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.606152
X-RAY DIFFRACTIONr_chiral_restr0.0720.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211610
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_it01.51386
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it022243
X-RAY DIFFRACTIONr_scbond_it03776
X-RAY DIFFRACTIONr_scangle_it04.5697
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
Rfree0.283 74 -
Rwork0.246 1182 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4963-0.1839-0.63582.3534-0.55012.5866-0.06290.35-0.168-0.24130.00690.15480.0812-0.30850.05610.0345-0.012-0.02050.1009-0.0190.025315.34820.26310.804
24.7869-1.805-0.17076.3739-0.66153.6996-0.3204-0.75470.29860.81070.2434-0.3532-0.06140.0670.0770.24260.0338-0.10110.1467-0.07230.13512.32313.1647.15
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 176
2X-RAY DIFFRACTION2B1 - 104

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