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- PDB-1x0r: Thioredoxin Peroxidase from Aeropyrum pernix K1 -

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Basic information

Entry
Database: PDB / ID: 1x0r
TitleThioredoxin Peroxidase from Aeropyrum pernix K1
ComponentsProbable peroxiredoxin
KeywordsOXIDOREDUCTASE / Thioredoxin Fold / 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
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsNakamura, T. / Yamamoto, T. / Inoue, T. / Matsumura, H. / Kobayashi, A. / Hagihara, Y. / Uegaki, K. / Ataka, M. / Kai, Y. / Ishikawa, K.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of thioredoxin peroxidase from aerobic hyperthermophilic archaeon Aeropyrum pernix K1
Authors: Nakamura, T. / Yamamoto, T. / Inoue, T. / Matsumura, H. / Kobayashi, A. / Hagihara, Y. / Uegaki, K. / Ataka, M. / Kai, Y. / Ishikawa, K.
History
DepositionMar 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,788138
Polymers287,84310
Non-polymers7,945128
Water21,4201189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: Probable peroxiredoxin
H: Probable peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,68620
Polymers57,5692
Non-polymers1,11718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint11 kcal/mol
Surface area18780 Å2
MethodPISA
3
E: Probable peroxiredoxin
F: Probable peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,36931
Polymers57,5692
Non-polymers1,80029
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint22 kcal/mol
Surface area18320 Å2
MethodPISA
4
I: Probable peroxiredoxin
J: Probable peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24529
Polymers57,5692
Non-polymers1,67627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint20 kcal/mol
Surface area19030 Å2
MethodPISA
5
C: Probable peroxiredoxin
D: Probable peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,18228
Polymers57,5692
Non-polymers1,61426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint11 kcal/mol
Surface area18690 Å2
MethodPISA
6
A: Probable peroxiredoxin
B: Probable peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,30730
Polymers57,5692
Non-polymers1,73828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint18 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.633, 101.792, 102.886
Angle α, β, γ (deg.)105.37, 105.28, 93.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Probable peroxiredoxin / Thioredoxin Peroxidase


Mass: 28784.340 Da / Num. of mol.: 10 / Mutation: C207S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE2278 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9Y9L0, peroxiredoxin
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 128 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: imidazole-HCl, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.984 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 28, 2004 / Details: Bending Magnet
RadiationMonochromator: Bending Magnet / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 569297 / Num. obs: 191063 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.98 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.188 / % possible all: 86.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.89 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 440565.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 9167 4.7 %RANDOM
Rwork0.164 ---
obs0.164 173623 89.9 %-
all-182790 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8912 Å2 / ksol: 0.371886 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-1.96 Å21.95 Å2
2---2.92 Å2-0.54 Å2
3---3.86 Å2
Refinement stepCycle: LAST / Resolution: 2→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19730 0 512 1189 21431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0461.5
X-RAY DIFFRACTIONc_angle_deg3.42
X-RAY DIFFRACTIONc_dihedral_angle_d25.22
X-RAY DIFFRACTIONc_improper_angle_d2.312.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 1396 4.5 %
Rwork0.206 47617 -
obs-28398 89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5tpx.paramtpx.top

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