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- PDB-6krm: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F46A mutant -

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Basic information

Entry
Database: PDB / ID: 6krm
TitlePeroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F46A 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)288,11920
Polymers286,19710
Non-polymers1,92110
Water25,6711425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54320 Å2
ΔGint-269 kcal/mol
Surface area77440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.996, 103.077, 104.801
Angle α, β, γ (deg.)105.801, 105.255, 92.531
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Peroxiredoxin / Thioredoxin peroxidase / ApTPx


Mass: 28619.734 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.: 1425 / 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: 53.75 %
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: 263527 / % possible obs: 97 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12878

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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→49.252 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.585 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 13337 5.063 %RANDOM
Rwork0.1633 ---
all0.165 ---
obs-263395 96.991 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.939 Å2
Baniso -1Baniso -2Baniso -3
1-0.097 Å2-1.197 Å21.123 Å2
2---1.569 Å2-1.08 Å2
3---1.181 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19670 0 130 1425 21225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01320330
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719080
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.64727650
X-RAY DIFFRACTIONr_angle_other_deg1.4511.57443970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78152430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.91419.8291170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.859153330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.59515220
X-RAY DIFFRACTIONr_chiral_restr0.0920.22570
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0222670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024710
X-RAY DIFFRACTIONr_nbd_refined0.2060.24216
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.219165
X-RAY DIFFRACTIONr_nbtor_refined0.1720.29940
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.29616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.21236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1410.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.233
X-RAY DIFFRACTIONr_nbd_other0.2850.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1450.21
X-RAY DIFFRACTIONr_mcbond_it2.0872.39750
X-RAY DIFFRACTIONr_mcbond_other2.0842.39749
X-RAY DIFFRACTIONr_mcangle_it2.8683.43812170
X-RAY DIFFRACTIONr_mcangle_other2.8683.43912171
X-RAY DIFFRACTIONr_scbond_it3.6952.76910580
X-RAY DIFFRACTIONr_scbond_other3.6952.76910577
X-RAY DIFFRACTIONr_scangle_it5.5223.95815480
X-RAY DIFFRACTIONr_scangle_other5.5223.95815481
X-RAY DIFFRACTIONr_lrange_it7.24827.91723377
X-RAY DIFFRACTIONr_lrange_other7.19227.56323096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.26810120.23618282X-RAY DIFFRACTION95.8042
1.847-1.8970.2579570.22217878X-RAY DIFFRACTION95.9256
1.897-1.9520.2359580.20817380X-RAY DIFFRACTION96.3181
1.952-2.0120.2419280.19916847X-RAY DIFFRACTION96.4512
2.012-2.0780.2249230.18416362X-RAY DIFFRACTION96.5157
2.078-2.1510.2138530.17515903X-RAY DIFFRACTION96.6153
2.151-2.2320.2138040.16315366X-RAY DIFFRACTION96.6123
2.232-2.3240.1927480.15714836X-RAY DIFFRACTION96.783
2.324-2.4270.217990.15414169X-RAY DIFFRACTION96.9116
2.427-2.5450.1927030.15513638X-RAY DIFFRACTION97.1612
2.545-2.6830.2036500.15613000X-RAY DIFFRACTION97.4374
2.683-2.8450.2196560.16312284X-RAY DIFFRACTION97.4618
2.845-3.0420.2026260.16111523X-RAY DIFFRACTION97.2231
3.042-3.2850.1895360.15510755X-RAY DIFFRACTION97.3614
3.285-3.5980.1835130.1599983X-RAY DIFFRACTION98.3048
3.598-4.0220.1674820.1399054X-RAY DIFFRACTION98.7368
4.022-4.6430.1494320.1337984X-RAY DIFFRACTION98.9536
4.643-5.6840.1733570.1486757X-RAY DIFFRACTION98.9705
5.684-8.0240.1942690.1685193X-RAY DIFFRACTION98.2374
8.024-49.2520.181310.1642864X-RAY DIFFRACTION97.8438

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