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- PDB-3tb2: 1-Cys peroxidoxin from Plasmodium Yoelli -

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Basic information

Entry
Database: PDB / ID: 3tb2
Title1-Cys peroxidoxin from Plasmodium Yoelli
Components1-Cys peroxiredoxin
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peroxiredoxin activity
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. / Thioredoxin domain ...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 / Resolution: 2.3 Å
AuthorsQiu, W. / Artz, J.D. / Vedadi, M. / Sharma, S. / Houston, S. / Lew, J. / Wasney, G. / Amani, M. / Xu, X. / Bray, J. ...Qiu, W. / Artz, J.D. / 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.D. / 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, ...Authors: Vedadi, M. / Lew, J. / Artz, J.D. / 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
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,59334
Polymers101,4414
Non-polymers2,15230
Water11,295627
1
A: 1-Cys peroxiredoxin
C: 1-Cys peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,93819
Polymers50,7212
Non-polymers1,21717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-32 kcal/mol
Surface area19000 Å2
MethodPISA
2
B: 1-Cys peroxiredoxin
D: 1-Cys peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,65515
Polymers50,7212
Non-polymers93513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-32 kcal/mol
Surface area18710 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: 25360.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Pet15 Tev Is a Modification of Pet15b (novagen) with Thrombin Site Replaced with Tev Site.
Source: (gene. exp.) Plasmodium yoelii (eukaryote) / Gene: py04285 / Plasmid: pET15-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86SB3
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2004
RadiationMonochromator: UNKNOWN / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 56255 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 44.44 Å2
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
ADSCQuantumdata collection
PHASESphasing
BUSTER2.8.0refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→78.42 Å / Cor.coef. Fo:Fc: 0.9529 / Cor.coef. Fo:Fc free: 0.9373 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 2858 5.08 %RANDOM
Rwork0.1658 ---
obs0.1677 56255 --
Displacement parametersBiso mean: 43.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.7583 Å20 Å20 Å2
2---6.0097 Å20 Å2
3---7.7679 Å2
Refine analyzeLuzzati coordinate error obs: 0.223 Å
Refinement stepCycle: LAST / Resolution: 2.3→78.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7092 0 133 627 7852
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017385HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.129946HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2585SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes180HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1015HARMONIC5
X-RAY DIFFRACTIONt_it7385HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion18.66
X-RAY DIFFRACTIONt_improper_torsion8HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion963SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8644SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2116 206 5.05 %
Rwork0.185 3873 -
all0.1864 4079 -

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