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- PDB-5xbs: Peroxiredoxin from Aeropyrum pernix (6m mutant) -

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Basic information

Entry
Database: PDB / ID: 5xbs
TitlePeroxiredoxin from Aeropyrum pernix (6m mutant)
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / dimer
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / 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 / 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
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.51 Å
AuthorsNakamura, T. / Uegaki, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology24109017 Japan
Japan Society for the Promotion of Science15K01815 Japan
CitationJournal: J. Biochem. / Year: 2017
Title: Alteration of molecular assembly of peroxiredoxins from hyperthermophilic archaea
Authors: Nakamura, T. / Oshima, M. / Yasuda, M. / Shimamura, A. / Morita, J. / Uegaki, K.
History
DepositionMar 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)114,5154
Polymers114,5154
Non-polymers00
Water724
1
A: Peroxiredoxin
B: Peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)57,2572
Polymers57,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-46 kcal/mol
Surface area19260 Å2
MethodPISA
2
C: Peroxiredoxin
D: Peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)57,2572
Polymers57,2572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-43 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.656, 170.788, 61.972
Angle α, β, γ (deg.)90.00, 114.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peroxiredoxin / Thioredoxin peroxidase / ApTPx


Mass: 28628.723 Da / Num. of mol.: 4 / Mutation: V23R, F80E, S81D, I83S, K84A, W210S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate (pH 6.5), 0.2 M magnesium acetate, and 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 28181 / % possible obs: 84.8 % / Redundancy: 4.4 % / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.51→36.33 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.864 / SU B: 9.645 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30048 1433 5.1 %RANDOM
Rwork0.21028 ---
obs0.21476 26722 84.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 46.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.17 Å2
2--0.94 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.51→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7771 0 0 4 7775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197981
X-RAY DIFFRACTIONr_bond_other_d0.0010.027618
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.95810844
X-RAY DIFFRACTIONr_angle_other_deg0.8323.00117476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2945958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74522.005384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.401151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5651594
X-RAY DIFFRACTIONr_chiral_restr0.0840.21175
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021889
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.509→2.574 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 108 -
Rwork0.328 1674 -
obs--71.8 %

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