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- PDB-6krq: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F80A mutant -

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Basic information

Entry
Database: PDB / ID: 6krq
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F80A mutant
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
Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 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 ...Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Peroxiredoxin
Similarity search - Component
Biological speciesAeropyrum pernix (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 Science19K21133 Japan
Japan Society for the Promotion of Science15K01815 Japan
CitationJournal: Protein Sci. / Year: 2020
Title: Disassembly of the ring-type decameric structure of peroxiredoxin from Aeropyrum pernix K1 by amino acid mutation.
Authors: Himiyama, T. / Nakamura, T.
History
DepositionAug 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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)280,32920
Polymers278,40810
Non-polymers1,92110
Water16,952941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53290 Å2
ΔGint-249 kcal/mol
Surface area78160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.148, 103.156, 105.346
Angle α, β, γ (deg.)106.095, 105.017, 92.404
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Peroxiredoxin / Thioredoxin peroxidase / ApTPx


Mass: 27840.793 Da / Num. of mol.: 10 / Mutation: C50S,F80A,C207S,C213S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / 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.: 941 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Ammonium phosphate monobasic

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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: 2.1→50 Å / Num. obs: 168524 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8311

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E2G

2e2g


Resolution: 2.1→49.231 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.992 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 8383 4.977 %RANDOM
Rwork0.1685 ---
all0.171 ---
obs-168437 97.703 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-1.043 Å21.711 Å2
2---2.085 Å2-1.498 Å2
3---0.998 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19670 0 130 941 20741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01320330
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719080
X-RAY DIFFRACTIONr_angle_refined_deg1.581.64727650
X-RAY DIFFRACTIONr_angle_other_deg1.3191.57443970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79952430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.62919.8291170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.058153330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.91515220
X-RAY DIFFRACTIONr_chiral_restr0.0740.22570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024710
X-RAY DIFFRACTIONr_nbd_refined0.20.24195
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.219044
X-RAY DIFFRACTIONr_nbtor_refined0.1680.29846
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.29470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2937
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0930.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.233
X-RAY DIFFRACTIONr_nbd_other0.2530.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.224
X-RAY DIFFRACTIONr_mcbond_it2.3233.0629750
X-RAY DIFFRACTIONr_mcbond_other2.3233.0629749
X-RAY DIFFRACTIONr_mcangle_it3.2854.57712170
X-RAY DIFFRACTIONr_mcangle_other3.2854.57712171
X-RAY DIFFRACTIONr_scbond_it3.6483.54910580
X-RAY DIFFRACTIONr_scbond_other3.6473.54810577
X-RAY DIFFRACTIONr_scangle_it5.5755.12515480
X-RAY DIFFRACTIONr_scangle_other5.5755.12515481
X-RAY DIFFRACTIONr_lrange_it7.25236.18622985
X-RAY DIFFRACTIONr_lrange_other7.24236.04622844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.2786180.23511751X-RAY DIFFRACTION96.784
2.155-2.2140.2745780.21911430X-RAY DIFFRACTION96.8465
2.214-2.2780.2535910.19411146X-RAY DIFFRACTION96.9359
2.278-2.3480.2415630.18310878X-RAY DIFFRACTION97.1387
2.348-2.4250.2495300.17710456X-RAY DIFFRACTION97.0924
2.425-2.510.2424990.17610283X-RAY DIFFRACTION97.3808
2.51-2.6040.2455100.1739772X-RAY DIFFRACTION97.5059
2.604-2.7110.2354960.1769534X-RAY DIFFRACTION97.5681
2.711-2.8310.264570.1859098X-RAY DIFFRACTION97.7894
2.831-2.9690.2374840.1768665X-RAY DIFFRACTION97.6623
2.969-3.130.2284350.1758291X-RAY DIFFRACTION97.8141
3.13-3.3190.224100.1697849X-RAY DIFFRACTION97.8554
3.319-3.5480.2033820.1567398X-RAY DIFFRACTION98.6934
3.548-3.8320.1943680.1516923X-RAY DIFFRACTION98.8208
3.832-4.1970.1923490.1426355X-RAY DIFFRACTION98.9082
4.197-4.6910.1613230.1265739X-RAY DIFFRACTION98.9876
4.691-5.4150.192800.1415091X-RAY DIFFRACTION99.0411
5.415-6.6270.2492170.1774291X-RAY DIFFRACTION98.9247
6.627-9.3510.1791960.1583299X-RAY DIFFRACTION99.0085
9.351-49.2310.273970.1981806X-RAY DIFFRACTION97.6899

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