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- PDB-7bvv: Crystal structure of sulfonic peroxiredoxin Ahp1 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7bvv
TitleCrystal structure of sulfonic peroxiredoxin Ahp1 in complex with thioredoxin Trx2
Components
  • Peroxiredoxin AHP1
  • Thioredoxin-2
KeywordsOXIDOREDUCTASE / peroxiredoxin / thioredoxin / alkyl hydroperoxide reductase / 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: 2.12 Å
AuthorsLian, F.M. / Jiang, Y.L. / Yang, W. / Yang, X.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Crystal structure of sulfonic peroxiredoxin Ahp1 in complex with thioredoxin Trx2 mimics a conformational intermediate during the catalytic cycle.
Authors: Lian, F.M. / Jiang, Y.L. / Yang, W. / Yang, X.
History
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Peroxiredoxin AHP1
B: Thioredoxin-2


Theoretical massNumber of molelcules
Total (without water)31,3952
Polymers31,3952
Non-polymers00
Water1,45981
1
A: Peroxiredoxin AHP1

A: Peroxiredoxin AHP1

B: Thioredoxin-2

B: Thioredoxin-2


Theoretical massNumber of molelcules
Total (without water)62,7914
Polymers62,7914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
crystal symmetry operation6_545-x+1/2,-y-1/2,z+1/21
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
Buried area3120 Å2
ΔGint-33 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.500, 132.800, 76.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-203-

HOH

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Components

#1: Protein Peroxiredoxin AHP1 / Prx / Alkyl hydroperoxide reductase / AHPC1 / Cytoplasmic thiol peroxidase 3 / cTPx 3 / Thiol- ...Prx / Alkyl hydroperoxide reductase / AHPC1 / Cytoplasmic thiol peroxidase 3 / cTPx 3 / Thiol-specific antioxidant II / TSA II / Thioredoxin peroxidase type II / TPx type II


Mass: 19180.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: AHP1, YLR109W, L2916, L9354.5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TRX2, TRX1, YGR209C, G7746 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P22803
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% polyethylene glycol 3,350, 0.2 M lithium sulfate, 0.1 M HEPES-NaOH, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 16850 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 30.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.035 / Rrim(I) all: 0.094 / Net I/σ(I): 14.8
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2424 / CC1/2: 0.904 / Rpim(I) all: 0.195 / Rrim(I) all: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DSS

4dss


Resolution: 2.12→38.525 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.195
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 824 4.895 %Random selection
Rwork0.2111 ---
all0.213 ---
obs-16833 99.958 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.033 Å2
Baniso -1Baniso -2Baniso -3
1--0.552 Å2-0 Å20 Å2
2---0.282 Å2-0 Å2
3---0.834 Å2
Refinement stepCycle: LAST / Resolution: 2.12→38.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 0 0 81 2201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132165
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172003
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.6362946
X-RAY DIFFRACTIONr_angle_other_deg2.3161.5774668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62625.58186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06615357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.755152
X-RAY DIFFRACTIONr_chiral_restr0.0660.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022412
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02410
X-RAY DIFFRACTIONr_nbd_refined0.2040.2368
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.21690
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21041
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0750.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.27
X-RAY DIFFRACTIONr_nbd_other0.1860.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5220.25
X-RAY DIFFRACTIONr_mcbond_it2.6653.4041110
X-RAY DIFFRACTIONr_mcbond_other2.6663.4021109
X-RAY DIFFRACTIONr_mcangle_it3.935.0951384
X-RAY DIFFRACTIONr_mcangle_other3.9295.0981385
X-RAY DIFFRACTIONr_scbond_it2.8913.621054
X-RAY DIFFRACTIONr_scbond_other2.8913.621054
X-RAY DIFFRACTIONr_scangle_it4.485.2811562
X-RAY DIFFRACTIONr_scangle_other4.4795.2811562
X-RAY DIFFRACTIONr_lrange_it5.91438.5072328
X-RAY DIFFRACTIONr_lrange_other5.91438.4942320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.1750.293590.2791173X-RAY DIFFRACTION100
2.175-2.2340.333590.2331117X-RAY DIFFRACTION100
2.234-2.2990.238510.2221110X-RAY DIFFRACTION100
2.299-2.370.268620.2321063X-RAY DIFFRACTION100
2.37-2.4470.365510.2291067X-RAY DIFFRACTION100
2.447-2.5330.316470.241985X-RAY DIFFRACTION100
2.533-2.6280.341470.235976X-RAY DIFFRACTION100
2.628-2.7350.278460.233942X-RAY DIFFRACTION100
2.735-2.8560.317410.236921X-RAY DIFFRACTION100
2.856-2.9950.246610.232846X-RAY DIFFRACTION100
2.995-3.1560.254380.237827X-RAY DIFFRACTION100
3.156-3.3460.234390.238785X-RAY DIFFRACTION100
3.346-3.5760.222430.22734X-RAY DIFFRACTION100
3.576-3.860.246300.21692X-RAY DIFFRACTION100
3.86-4.2250.177350.166646X-RAY DIFFRACTION99.8534
4.225-4.7180.161350.154577X-RAY DIFFRACTION100
4.718-5.4370.197290.173515X-RAY DIFFRACTION100
5.437-6.6320.248290.191445X-RAY DIFFRACTION100
6.632-9.2710.164120.175362X-RAY DIFFRACTION100
9.271-38.5250.241100.189226X-RAY DIFFRACTION98.7448

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