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

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Basic information

Entry
Database: PDB / ID: 6krk
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys 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 K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)288,88020
Polymers286,95810
Non-polymers1,92110
Water22,0681225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.825, 102.790, 104.435
Angle α, β, γ (deg.)105.878, 105.135, 92.463
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Peroxiredoxin / Thioredoxin peroxidase / ApTPx


Mass: 28695.828 Da / Num. of mol.: 10
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.: 1225 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
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: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 262648 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 12843

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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: 1.8→49.432 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.441 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 13261 5.058 %RANDOM
Rwork0.1588 ---
all0.161 ---
obs-262196 97.357 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.435 Å2-0.706 Å21.284 Å2
2---1.488 Å2-1.603 Å2
3---1.024 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19730 0 130 1225 21085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01320400
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719120
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.64727740
X-RAY DIFFRACTIONr_angle_other_deg1.4791.57444060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56752430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.95819.8311180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.693153340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9115220
X-RAY DIFFRACTIONr_chiral_restr0.0980.22570
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222740
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024760
X-RAY DIFFRACTIONr_nbd_refined0.2110.24343
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.219455
X-RAY DIFFRACTIONr_nbtor_refined0.1740.29988
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0990.29836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.21050
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.180.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.236
X-RAY DIFFRACTIONr_nbd_other0.2890.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2940.229
X-RAY DIFFRACTIONr_mcbond_it2.1212.3349750
X-RAY DIFFRACTIONr_mcbond_other2.1212.3339749
X-RAY DIFFRACTIONr_mcangle_it2.9153.48812170
X-RAY DIFFRACTIONr_mcangle_other2.9153.48812171
X-RAY DIFFRACTIONr_scbond_it3.9322.82610650
X-RAY DIFFRACTIONr_scbond_other3.9312.82610647
X-RAY DIFFRACTIONr_scangle_it5.8384.03715570
X-RAY DIFFRACTIONr_scangle_other5.8384.03715571
X-RAY DIFFRACTIONr_lrange_it7.51828.39423382
X-RAY DIFFRACTIONr_lrange_other7.4628.08523153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.25810120.2218080X-RAY DIFFRACTION95.9011
1.847-1.8970.2449450.20717753X-RAY DIFFRACTION95.9758
1.897-1.9520.2229540.19417256X-RAY DIFFRACTION96.5075
1.952-2.0120.2169210.18416785X-RAY DIFFRACTION96.7277
2.012-2.0780.229100.17616330X-RAY DIFFRACTION96.9574
2.078-2.1510.218780.1715808X-RAY DIFFRACTION96.9665
2.151-2.2320.2067560.15715381X-RAY DIFFRACTION97.1348
2.232-2.3240.1877610.14914724X-RAY DIFFRACTION97.2554
2.324-2.4270.1997980.1514145X-RAY DIFFRACTION97.4946
2.427-2.5450.1966970.15313615X-RAY DIFFRACTION97.7529
2.545-2.6830.2076460.15412967X-RAY DIFFRACTION97.9564
2.683-2.8450.2186560.16212222X-RAY DIFFRACTION97.8795
2.845-3.0420.1976240.16211509X-RAY DIFFRACTION97.8705
3.042-3.2850.1765340.14910727X-RAY DIFFRACTION97.7348
3.285-3.5980.1725030.159956X-RAY DIFFRACTION98.7816
3.598-4.0220.1694780.149001X-RAY DIFFRACTION98.9457
4.022-4.6430.1484340.1327910X-RAY DIFFRACTION98.9446
4.643-5.6840.183490.1466720X-RAY DIFFRACTION99.2419
5.684-8.0240.2072720.1745204X-RAY DIFFRACTION99.0773
8.024-49.4320.1861330.1742842X-RAY DIFFRACTION98.0554

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