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- PDB-6krp: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A mutant -

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Basic information

Entry
Database: PDB / ID: 6krp
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A mutant
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / Peroxiredoxin
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / antioxidant activity / cellular response to hydrogen peroxide / identical protein binding / cytoplasm
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 / Thioredoxin domain profile. ...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: 1.89 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)287,72820
Polymers285,80710
Non-polymers1,92110
Water29,4181633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54840 Å2
ΔGint-277 kcal/mol
Surface area77860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.240, 103.285, 105.129
Angle α, β, γ (deg.)105.779, 105.245, 92.446
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Peroxiredoxin / / Thioredoxin peroxidase / ApTPx


Mass: 28580.699 Da / Num. of mol.: 10 / Mutation: C50S,W88A,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 / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 1633 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: 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: 1.89→50 Å / Num. obs: 230604 / % possible obs: 97.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.3
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 11353

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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: 1.89→49.368 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.946 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.114
RfactorNum. reflection% reflection
Rfree0.1883 11796 5.115 %
Rwork0.1639 --
all0.165 --
obs-230599 97.424 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.694 Å2
Baniso -1Baniso -2Baniso -3
1-0.223 Å2-0.808 Å21.136 Å2
2---1.648 Å2-0.953 Å2
3---1.055 Å2
Refinement stepCycle: LAST / Resolution: 1.89→49.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19622 0 130 1633 21385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01320270
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719051
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.64727553
X-RAY DIFFRACTIONr_angle_other_deg1.3921.57443905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92652427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.05419.8291170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61153330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.04315220
X-RAY DIFFRACTIONr_chiral_restr0.0890.22568
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0222619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024697
X-RAY DIFFRACTIONr_nbd_refined0.2110.24139
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.218516
X-RAY DIFFRACTIONr_nbtor_refined0.1680.29745
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.28948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.21281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1160.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.241
X-RAY DIFFRACTIONr_nbd_other0.2490.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4070.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3160.23
X-RAY DIFFRACTIONr_mcbond_it2.6282.7089738
X-RAY DIFFRACTIONr_mcbond_other2.6272.7079737
X-RAY DIFFRACTIONr_mcangle_it3.6854.03612155
X-RAY DIFFRACTIONr_mcangle_other3.6854.03712156
X-RAY DIFFRACTIONr_scbond_it3.9753.16110532
X-RAY DIFFRACTIONr_scbond_other3.9723.1610529
X-RAY DIFFRACTIONr_scangle_it5.9244.54615398
X-RAY DIFFRACTIONr_scangle_other5.9244.54615399
X-RAY DIFFRACTIONr_lrange_it8.14832.37723041
X-RAY DIFFRACTIONr_lrange_other8.11631.93222684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.9390.2598930.2416074X-RAY DIFFRACTION96.3268
1.939-1.9920.2578140.22315639X-RAY DIFFRACTION96.5155
1.992-2.050.2327810.215255X-RAY DIFFRACTION96.7131
2.05-2.1130.2148270.19314802X-RAY DIFFRACTION96.864
2.113-2.1820.2198100.18214321X-RAY DIFFRACTION97.0371
2.182-2.2590.2018180.16713845X-RAY DIFFRACTION97.1574
2.259-2.3440.1796800.15413530X-RAY DIFFRACTION97.3288
2.344-2.440.1887480.15512953X-RAY DIFFRACTION97.5091
2.44-2.5480.1836750.15212436X-RAY DIFFRACTION97.6465
2.548-2.6720.1895890.16211993X-RAY DIFFRACTION97.8383
2.672-2.8170.2015970.16311388X-RAY DIFFRACTION98.0448
2.817-2.9880.1925510.16410755X-RAY DIFFRACTION98.0913
2.988-3.1940.195260.16110100X-RAY DIFFRACTION97.4594
3.194-3.4490.1854650.1629267X-RAY DIFFRACTION96.2516
3.449-3.7780.1684630.1538711X-RAY DIFFRACTION98.6028
3.778-4.2230.1564600.1377857X-RAY DIFFRACTION98.8472
4.223-4.8750.1553950.1296955X-RAY DIFFRACTION98.9233
4.875-5.9670.1673170.1535893X-RAY DIFFRACTION99.0273
5.967-8.4230.1832540.1724532X-RAY DIFFRACTION98.9866
8.423-49.3680.181330.1882498X-RAY DIFFRACTION98.2083

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