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- PDB-2h66: The Crystal Structure of Plasmodium Vivax 2-Cys peroxiredoxin -

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Basic information

Entry
Database: PDB / ID: 2h66
TitleThe Crystal Structure of Plasmodium Vivax 2-Cys peroxiredoxin
ComponentsPV-PF14_0368
KeywordsSTRUCTURAL GENOMICS/OXIDOREDUCTASE / plasmodium / vivax / peroxiredoxin / Structural Genomics / Structural Genomics Consortium / SGC / STRUCTURAL GENOMICS-OXIDOREDUCTASE COMPLEX
Function / homology
Function and homology information


thioredoxin peroxidase activity / cellular response to stress / cell redox homeostasis / hydrogen peroxide catabolic process / 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 ...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
2-Cys peroxiredoxin, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWernimont, A.K. / Dong, A. / Zhao, Y. / Lew, J. / Melone, M. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. ...Wernimont, A.K. / Dong, A. / Zhao, Y. / Lew, J. / Melone, M. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R. / Artz, J.D. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionMay 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Currently, there is no aminoacid sequence database reference available for the protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PV-PF14_0368
B: PV-PF14_0368
C: PV-PF14_0368
D: PV-PF14_0368
E: PV-PF14_0368
F: PV-PF14_0368
G: PV-PF14_0368
H: PV-PF14_0368
I: PV-PF14_0368
J: PV-PF14_0368


Theoretical massNumber of molelcules
Total (without water)237,32110
Polymers237,32110
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20520 Å2
ΔGint-154 kcal/mol
Surface area66780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.550, 149.590, 131.910
Angle α, β, γ (deg.)90.00, 104.88, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a pentagonal ring of dimers, as seen in the asymmetric unit.

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Components

#1: Protein
PV-PF14_0368


Mass: 23732.133 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: pET28 LIC/TEV DER / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus/RIL / References: UniProt: A5K421
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5% PEG 4000, 50 mM NaAc, 100 mM NaAC, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→41.56 Å / Num. all: 91258 / Num. obs: 86441 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.098 / Net I/σ(I): 10.8
Reflection shellResolution: 2.48→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.3 / Num. unique all: 5688 / Rsym value: 0.498 / % possible all: 99.8

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Processing

Software
NameClassification
ADSCdata collection
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMV

1qmv


Resolution: 2.5→41.56 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23205 4302 -RANDOM
Rwork0.1944 ---
all0.1963 86715 --
obs0.1963 82137 94.72 %-
Displacement parametersBiso mean: 45.744 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.3 Å2
2---0.15 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13294 0 0 154 13448
LS refinement shellResolution: 2.5→2.565 Å
RfactorNum. reflection% reflection
Rfree0.345 264 -
Rwork0.304 --
obs-5347 84.1 %

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