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- PDB-7c87: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C2... -

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Basic information

Entry
Database: PDB / ID: 7c87
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant (ApPrx*F80C)
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 / Peroxiredoxin
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)288,43920
Polymers286,51810
Non-polymers1,92110
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53200 Å2
ΔGint-275 kcal/mol
Surface area77440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.065, 103.134, 104.956
Angle α, β, γ (deg.)106.026, 104.752, 92.595
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-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 896 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 53.59 %
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: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 146036 / % possible obs: 97.7 % / Redundancy: 2.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7276 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KRK

6krk


Resolution: 2.2→49.227 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.108 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2072 7443 5.107 %
Rwork0.1564 138301 -
all0.159 --
obs-145744 97.546 %
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: 44.523 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å2-0.002 Å20.004 Å2
2---0.005 Å2-0.002 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19680 0 130 896 20706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01320340
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719070
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.64727660
X-RAY DIFFRACTIONr_angle_other_deg1.3041.57543960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87652430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.5819.8291170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.519153340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.55415220
X-RAY DIFFRACTIONr_chiral_restr0.0760.22570
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024710
X-RAY DIFFRACTIONr_nbd_refined0.2030.24182
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.219129
X-RAY DIFFRACTIONr_nbtor_refined0.1680.29791
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.29812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2856
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.226
X-RAY DIFFRACTIONr_nbd_other0.2430.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.222
X-RAY DIFFRACTIONr_mcbond_it3.3984.3859750
X-RAY DIFFRACTIONr_mcbond_other3.3974.3849749
X-RAY DIFFRACTIONr_mcangle_it4.4996.5612170
X-RAY DIFFRACTIONr_mcangle_other4.4996.56112171
X-RAY DIFFRACTIONr_scbond_it4.7074.9410590
X-RAY DIFFRACTIONr_scbond_other4.7074.9410587
X-RAY DIFFRACTIONr_scangle_it6.9037.18115490
X-RAY DIFFRACTIONr_scangle_other6.9037.18115491
X-RAY DIFFRACTIONr_lrange_it8.59551.25722822
X-RAY DIFFRACTIONr_lrange_other8.59151.10722698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.2635600.20810162X-RAY DIFFRACTION96.5772
2.257-2.3190.2355190.1859891X-RAY DIFFRACTION96.6305
2.319-2.3860.2295300.1769610X-RAY DIFFRACTION96.6451
2.386-2.460.2214980.1699367X-RAY DIFFRACTION96.9247
2.46-2.540.2384510.1759057X-RAY DIFFRACTION96.9512
2.54-2.6290.2455040.1838791X-RAY DIFFRACTION97.096
2.629-2.7280.2544490.1748526X-RAY DIFFRACTION97.4802
2.728-2.840.264380.1818190X-RAY DIFFRACTION97.5025
2.84-2.9660.2324290.177820X-RAY DIFFRACTION97.6907
2.966-3.110.2314000.1697537X-RAY DIFFRACTION97.6862
3.11-3.2790.2254060.1597161X-RAY DIFFRACTION97.6639
3.279-3.4770.2193400.1626803X-RAY DIFFRACTION97.7957
3.477-3.7170.2163350.1526373X-RAY DIFFRACTION98.3866
3.717-4.0140.1723430.1385997X-RAY DIFFRACTION98.8309
4.014-4.3970.1672850.1285502X-RAY DIFFRACTION98.9062
4.397-4.9140.1642710.124998X-RAY DIFFRACTION98.837
4.914-5.6720.1772330.1374399X-RAY DIFFRACTION99.0167
5.672-6.9410.1992000.1493728X-RAY DIFFRACTION98.7431
6.941-9.7920.1441640.1262832X-RAY DIFFRACTION98.6825
9.792-49.2270.193880.1921557X-RAY DIFFRACTION96.651

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