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- PDB-2e2g: Crystal structure of archaeal peroxiredoxin, thioredoxin peroxida... -

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Basic information

Entry
Database: PDB / ID: 2e2g
TitleCrystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (pre-oxidation form)
ComponentsProbable peroxiredoxin
KeywordsOXIDOREDUCTASE / thioredoxin peroxidase / cysteine sulfenic acid / cysteine sulfinic acid / cysteine sulfonic acid / hypervalent sulfur compound / peroxidatic cysteine
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
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNakamura, T. / Yamamoto, T. / Abe, M. / Matsumura, H. / Hagihara, Y. / Goto, T. / Yamaguchi, T. / Inoue, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Authors: Nakamura, T. / Yamamoto, T. / Abe, M. / Matsumura, H. / Hagihara, Y. / Goto, T. / Yamaguchi, T. / Inoue, T.
History
DepositionNov 13, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable peroxiredoxin
B: Probable peroxiredoxin
C: Probable peroxiredoxin
D: Probable peroxiredoxin
E: Probable peroxiredoxin
F: Probable peroxiredoxin
G: Probable peroxiredoxin
H: Probable peroxiredoxin
I: Probable peroxiredoxin
J: Probable peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)287,28010
Polymers287,28010
Non-polymers00
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46050 Å2
ΔGint-305 kcal/mol
Surface area79320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.204, 103.353, 104.632
Angle α, β, γ (deg.)105.79, 105.19, 92.68
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Probable peroxiredoxin / Thioredoxin peroxidase


Mass: 28727.957 Da / Num. of mol.: 10 / Mutation: C207S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9Y9L0, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M Acetate buffer pH4.8, 0.2M calcium chloride, 10%(v/v)isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 115754 / % possible obs: 87.2 % / Redundancy: 2.4 %
Reflection shellResolution: 2.4→2.49 Å / % possible all: 71.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X0R

1x0r


Resolution: 2.4→19.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.413 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22946 5036 5 %RANDOM
Rwork0.15293 ---
obs0.15675 95723 86.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19336 0 0 542 19878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02219877
X-RAY DIFFRACTIONr_angle_refined_deg2.141.95827023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00752362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99522.019941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.887153302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.26115220
X-RAY DIFFRACTIONr_chiral_restr0.1340.22932
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215304
X-RAY DIFFRACTIONr_nbd_refined0.2390.29630
X-RAY DIFFRACTIONr_nbtor_refined0.3220.213461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2941
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.211
X-RAY DIFFRACTIONr_mcbond_it1.2331.512271
X-RAY DIFFRACTIONr_mcangle_it1.971219386
X-RAY DIFFRACTIONr_scbond_it3.26238825
X-RAY DIFFRACTIONr_scangle_it5.1754.57637
LS refinement shellResolution: 2.4→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 292 -
Rwork0.182 5274 -
obs--65.71 %

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