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- PDB-2h01: PY00414- Plasmodium yoelii thioredoxin peroxidase I -

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Basic information

Entry
Database: PDB / ID: 2h01
TitlePY00414- Plasmodium yoelii thioredoxin peroxidase I
Components2-CYS PEROXIREDOXIN
KeywordsOXIDOREDUCTASE / THIOREDOXIN PEROXIDASE / STRUCTURAL GENOMICS / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


peroxiredoxin / cellular response to stress / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress / cytosol
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
thioredoxin-dependent peroxiredoxin / 2-Cys peroxiredoxin
Similarity search - Component
Biological speciesPlasmodium yoelii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsArtz, J. / Qiu, W. / Min, J.R. / Dong, A. / Lew, J. / Melone, M. / Alam, Z. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. ...Artz, J. / Qiu, W. / Min, J.R. / Dong, A. / Lew, J. / Melone, M. / Alam, Z. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of PY00414 - a Plasmodium yoelii thioredoxin peroxidase I
Authors: Artz, J. / Qiu, W. / Min, J.R. / Dong, A. / Lew, J. / Melone, M. / Alam, Z. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R.
History
DepositionMay 12, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionMay 30, 2006ID: 2FEG
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-CYS PEROXIREDOXIN


Theoretical massNumber of molelcules
Total (without water)21,3701
Polymers21,3701
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.076, 105.076, 41.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein 2-CYS PEROXIREDOXIN / E.C.1.11.1.-


Mass: 21370.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: Q86SB2, UniProt: Q7RSE5*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.6 M AMMONIUM SULFATE, 100 HEPES, PH 6.8, 200 MM NAAC, 20 MM NABR, 5% ETHYLENE GLYCOL, , VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 1, 2005
RadiationMonochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 10337 / Num. obs: 10337 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.36 Å / % possible all: 91.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZOF

1zof


Resolution: 2.3→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 542 random
Rwork0.258 --
all0.264 10337 -
obs0.258 10337 -
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 0 54 1422

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