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- PDB-8hh0: Peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C... -

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Basic information

Entry
Database: PDB / ID: 8hh0
TitlePeroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F42C)
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / Peroxiredoxin
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / cell redox homeostasis / peroxidase activity / cytosol
Similarity search - Function
Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / : / 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 ...Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / : / 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
1-naphthalen-2-ylethanone / Peroxiredoxin
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHimiyama, T. / Hamaguchi, T. / Yonekura, K. / Nakamura, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K15403 Japan
Japan Society for the Promotion of Science (JSPS)20K05740 Japan
Japan Agency for Medical Research and Development (AMED)jp22ama121006 Japan
Japan Science and TechnologyJPMJMI20G5 Japan
CitationJournal: Bioconjug Chem / Year: 2023
Title: Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins.
Authors: Tomoki Himiyama / Tasuku Hamaguchi / Koji Yonekura / Tsutomu Nakamura /
Abstract: In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein ...In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein interface. For the redesign of a natural protein assembly, a scrap-and-build approach employing chemical modification was used. Two different protein dimer units were designed based on peroxiredoxin from , which originally forms a dodecameric hexagonal ring with six homodimers. The two dimeric mutants were reorganized into a ring by reconstructing the protein-protein interactions via synthetic naphthalene moieties introduced by chemical modification. Cryo-electron microscopy revealed the formation of a uniquely shaped dodecameric hexagonal protein ring with broken symmetry, distorted from the regular hexagon of the wild-type protein. The artificially installed naphthalene moieties were arranged at the interfaces of dimer units, forming two distinct protein-protein interactions, one of which is highly unnatural. This study deciphered the potential of the chemical modification technique that constructs semiartificial protein structures and assembly hardly accessible by conventional amino acid mutations.
History
DepositionNov 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin
B: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5114
Polymers49,1702
Non-polymers3402
Water82946
1
A: Peroxiredoxin
B: Peroxiredoxin
hetero molecules

A: Peroxiredoxin
B: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0218
Polymers98,3414
Non-polymers6814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area11670 Å2
ΔGint-81 kcal/mol
Surface area34970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.090, 61.090, 236.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Peroxiredoxin / Thioredoxin peroxidase / Thioredoxin-dependent peroxiredoxin


Mass: 24585.143 Da / Num. of mol.: 2 / Mutation: F42C,C46S,C205S,C211S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: TK0537 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JF30, thioredoxin-dependent peroxiredoxin
#2: Chemical ChemComp-FL3 / 1-naphthalen-2-ylethanone


Mass: 170.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate 0.1 M sodium acetate (pH 4.6) 30% w/v polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→48.367 Å / Num. obs: 19657 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.985 / Rmerge(I) obs: 0.166 / Net I/σ(I): 6.4
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.603 / Num. unique obs: 1863 / CC1/2: 0.816

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IU0

6iu0


Resolution: 2.35→48.367 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.275 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.263
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2529 1021 5.201 %
Rwork0.2049 18610 -
all0.207 --
obs-19631 99.797 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 52.349 Å2
Baniso -1Baniso -2Baniso -3
1--0.195 Å20 Å20 Å2
2---0.195 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 26 46 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173386
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6384828
X-RAY DIFFRACTIONr_angle_other_deg1.2271.5837834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36223.218174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00415614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7671516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02776
X-RAY DIFFRACTIONr_nbd_refined0.1940.2727
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23203
X-RAY DIFFRACTIONr_nbtor_refined0.170.21712
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0960.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.217
X-RAY DIFFRACTIONr_nbd_other0.1940.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.24
X-RAY DIFFRACTIONr_mcbond_it3.7385.2691710
X-RAY DIFFRACTIONr_mcbond_other3.735.2691709
X-RAY DIFFRACTIONr_mcangle_it5.0387.9042134
X-RAY DIFFRACTIONr_mcangle_other5.0387.9042135
X-RAY DIFFRACTIONr_scbond_it4.3265.7221846
X-RAY DIFFRACTIONr_scbond_other4.3255.7241847
X-RAY DIFFRACTIONr_scangle_it6.4088.3982694
X-RAY DIFFRACTIONr_scangle_other6.4068.42695
X-RAY DIFFRACTIONr_lrange_it7.67861.0143977
X-RAY DIFFRACTIONr_lrange_other7.66861.0063976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.334630.3021326X-RAY DIFFRACTION100
2.411-2.4770.378840.291307X-RAY DIFFRACTION100
2.477-2.5490.363680.2681290X-RAY DIFFRACTION100
2.549-2.6270.282480.2391248X-RAY DIFFRACTION99.7691
2.627-2.7130.287600.2351185X-RAY DIFFRACTION99.9197
2.713-2.8080.324700.2381171X-RAY DIFFRACTION100
2.808-2.9140.279780.221128X-RAY DIFFRACTION100
2.914-3.0320.31600.2291075X-RAY DIFFRACTION99.912
3.032-3.1670.362650.2311040X-RAY DIFFRACTION99.9096
3.167-3.3210.253640.231993X-RAY DIFFRACTION99.9055
3.321-3.50.309560.227961X-RAY DIFFRACTION99.9018
3.5-3.7110.256540.221906X-RAY DIFFRACTION99.7921
3.711-3.9670.239500.199851X-RAY DIFFRACTION99.4481
3.967-4.2830.189340.171821X-RAY DIFFRACTION99.3031
4.283-4.6890.116340.149765X-RAY DIFFRACTION99.7503
4.689-5.2380.26410.175682X-RAY DIFFRACTION99.8619
5.238-6.0410.266290.191615X-RAY DIFFRACTION99.6904
6.041-7.3790.158240.151540X-RAY DIFFRACTION99.4709
7.379-10.3560.132250.126431X-RAY DIFFRACTION99.1304
10.356-48.3670.19140.188275X-RAY DIFFRACTION97.6351

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