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- PDB-1xcc: 1-Cys peroxidoxin from Plasmodium Yoelli -

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Basic information

Entry
Database: PDB / ID: 1xcc
Title1-Cys peroxidoxin from Plasmodium Yoelli
Components1-Cys peroxiredoxin
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomics Consortium / SGC
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
Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 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 / 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 speciesPlasmodium yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsVedadi, M. / Sharma, S. / Houston, S. / Lew, J. / Wasney, G. / Amani, M. / Xu, X. / Bray, J. / Sundstrom, M. / Arrowsmith, C. ...Vedadi, M. / Sharma, S. / Houston, S. / Lew, J. / Wasney, G. / Amani, M. / Xu, X. / Bray, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Hui, R. / Bochkarev, A. / 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
DepositionSep 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-Cys peroxiredoxin
B: 1-Cys peroxiredoxin
C: 1-Cys peroxiredoxin
D: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)101,3134
Polymers101,3134
Non-polymers00
Water5,765320
1
A: 1-Cys peroxiredoxin
C: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)50,6572
Polymers50,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-32 kcal/mol
Surface area19290 Å2
MethodPISA
2
B: 1-Cys peroxiredoxin
D: 1-Cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)50,6572
Polymers50,6572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-29 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.390, 156.842, 178.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
1-Cys peroxiredoxin


Mass: 25328.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii (eukaryote)
Description: pET15-TEV is a modification of pET15B (Novagen) with thrombin site replaced with TEV site.
Gene: PY04285 / Plasmid: pET15-TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q86SB3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 22% Peg 3350, 0.1M Bis-Tris pH 5.5, 0.2M Lithium Sulfate, 5% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97939, 0.97952, 0.96415
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2004
RadiationMonochromator: APS 17ID / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.979521
30.964151
ReflectionResolution: 2.3→20 Å / Num. obs: 53397 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.059 / Net I/σ(I): 24
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.038 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2858 5.1 %RANDOM
Rwork0.183 ---
obs0.185 53397 99.7 %-
all-53397 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--1.44 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7042 0 0 320 7362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227212
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9679756
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9815867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4225.096314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.601151338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3331520
X-RAY DIFFRACTIONr_chiral_restr0.1240.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025318
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.23134
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24874
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2399
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2061.54506
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96127101
X-RAY DIFFRACTIONr_scbond_it3.11433149
X-RAY DIFFRACTIONr_scangle_it4.5794.52655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 205 -
Rwork0.202 3852 -
obs--100 %

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