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- PDB-7c8a: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C2... -

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Basic information

Entry
Database: PDB / ID: 7c8a
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant modified with 2-(bromoacetyl)naphthalene(Naph@ApPrx*)
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / Peroxiredoxin
Function / homology
Function and homology information


peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / antioxidant activity / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / identical protein binding / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
CITRIC ACID / 1-naphthalen-2-ylethanone / Peroxiredoxin
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHimiyama, T. / Nakamura, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K21133 Japan
Japan Society for the Promotion of Science (JSPS)20K15403 Japan
CitationJournal: Bioconjug.Chem. / Year: 2021
Title: Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification.
Authors: Himiyama, T. / Tsuchiya, Y. / Yonezawa, Y. / Nakamura, T.
History
DepositionMay 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
F: Peroxiredoxin
G: Peroxiredoxin
H: Peroxiredoxin
I: Peroxiredoxin
J: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,14130
Polymers286,51810
Non-polymers3,62320
Water15,385854
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50630 Å2
ΔGint-280 kcal/mol
Surface area78850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.999, 103.081, 105.029
Angle α, β, γ (deg.)105.936, 104.945, 92.381
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Peroxiredoxin / Thioredoxin peroxidase / ApTPx


Mass: 28651.797 Da / Num. of mol.: 10 / Mutation: C50S, F80C, C207S, C213S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Strain: K1 / Gene: APE_2278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y9L0, peroxiredoxin
#2: Chemical
ChemComp-FL3 / 1-naphthalen-2-ylethanone


Mass: 170.207 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C12H10O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The reservoir solution contained 0.10 M sodium citrate (pH5.5) 0.20 M lithium sulfate 15% (v/v) reagent alcohol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 169516 / % possible obs: 98.1 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8322 / CC1/2: 0.833

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KRK

6krk


Resolution: 2.1→49.244 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.967 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2172 8444 4.986 %
Rwork0.1661 160920 -
all0.169 --
obs-169364 97.842 %
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: 39.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å20.004 Å20 Å2
2--0.005 Å20.003 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19680 0 260 854 20794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01320490
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719180
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.65727870
X-RAY DIFFRACTIONr_angle_other_deg2.0971.58244180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95752430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.59919.8291170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.229153340
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg14.6291510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.59315220
X-RAY DIFFRACTIONr_chiral_restr0.0750.22570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024780
X-RAY DIFFRACTIONr_nbd_refined0.2040.24384
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.219382
X-RAY DIFFRACTIONr_nbtor_refined0.170.29828
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.29532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2877
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1030.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3060.232
X-RAY DIFFRACTIONr_nbd_other0.2550.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2650.223
X-RAY DIFFRACTIONr_mcbond_it2.9043.839750
X-RAY DIFFRACTIONr_mcbond_other2.9033.8299749
X-RAY DIFFRACTIONr_mcangle_it3.9885.72712170
X-RAY DIFFRACTIONr_mcangle_other3.9875.72812171
X-RAY DIFFRACTIONr_scbond_it4.144.35810740
X-RAY DIFFRACTIONr_scbond_other4.1394.35810737
X-RAY DIFFRACTIONr_scangle_it6.2176.33815700
X-RAY DIFFRACTIONr_scangle_other6.2176.33815701
X-RAY DIFFRACTIONr_lrange_it8.03845.20623330
X-RAY DIFFRACTIONr_lrange_other8.03345.10723235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.094-2.1480.3096130.2711637X-RAY DIFFRACTION95.6807
2.148-2.2070.2745900.23711551X-RAY DIFFRACTION97.2447
2.207-2.2710.2726010.21711222X-RAY DIFFRACTION97.4932
2.271-2.3410.2535520.19710975X-RAY DIFFRACTION97.5542
2.341-2.4180.2575410.19110569X-RAY DIFFRACTION97.5931
2.418-2.5030.2525050.18210343X-RAY DIFFRACTION97.8708
2.503-2.5970.2315110.1789876X-RAY DIFFRACTION97.9536
2.597-2.7030.2335050.1729607X-RAY DIFFRACTION98.1462
2.703-2.8230.2384640.1769224X-RAY DIFFRACTION98.2157
2.823-2.9610.2244790.178741X-RAY DIFFRACTION98.3572
2.961-3.1210.2454460.1758346X-RAY DIFFRACTION98.4326
3.121-3.310.2244190.1647956X-RAY DIFFRACTION98.5874
3.31-3.5380.2113780.1587420X-RAY DIFFRACTION98.3727
3.538-3.8210.23590.156756X-RAY DIFFRACTION96.0448
3.821-4.1850.1813540.146341X-RAY DIFFRACTION98.3257
4.185-4.6780.1633240.1225766X-RAY DIFFRACTION99.0244
4.678-5.40.1732870.1315107X-RAY DIFFRACTION99.2639
5.4-6.6090.2222210.1634329X-RAY DIFFRACTION99.2799
6.609-9.3250.1811960.1473324X-RAY DIFFRACTION99.4069
9.325-49.2440.246990.1781830X-RAY DIFFRACTION98.5692

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