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- PDB-3tue: The structure of tryparedoxin peroxidase I from Leishmania major -

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Basic information

Entry
Database: PDB / ID: 3tue
TitleThe structure of tryparedoxin peroxidase I from Leishmania major
ComponentsTryparedoxin peroxidase
KeywordsOXIDOREDUCTASE / Thioredoxin fold / peroxidase / peroxiredoxin
Function / homology
Function and homology information


peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cilium / nucleoplasm / cytosol / cytoplasm
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
Tryparedoxin peroxidase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFiorillo, A. / Ilari, A. / Colotti, G.
CitationJournal: Plos Negl Trop Dis / Year: 2012
Title: The crystal structures of the tryparedoxin-tryparedoxin peroxidase couple unveil the structural determinants of leishmania detoxification pathway.
Authors: Fiorillo, A. / Colotti, G. / Boffi, A. / Baiocco, P. / Ilari, A.
History
DepositionSep 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Tryparedoxin peroxidase
B: Tryparedoxin peroxidase
C: Tryparedoxin peroxidase
D: Tryparedoxin peroxidase
E: Tryparedoxin peroxidase


Theoretical massNumber of molelcules
Total (without water)121,6645
Polymers121,6645
Non-polymers00
Water1,13563
1
A: Tryparedoxin peroxidase
B: Tryparedoxin peroxidase
C: Tryparedoxin peroxidase
D: Tryparedoxin peroxidase
E: Tryparedoxin peroxidase

A: Tryparedoxin peroxidase
B: Tryparedoxin peroxidase
C: Tryparedoxin peroxidase
D: Tryparedoxin peroxidase
E: Tryparedoxin peroxidase


Theoretical massNumber of molelcules
Total (without water)243,32810
Polymers243,32810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area16700 Å2
ΔGint-96 kcal/mol
Surface area65000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.977, 212.385, 90.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.42762, -0.870841, 0.24244), (-0.874509, 0.330633, -0.354845), (0.228855, -0.363755, -0.902944)29.50735, 21.79847, 9.414
3given(0.416503, 0.870742, -0.261407), (-0.867662, 0.294863, -0.400272), (-0.271454, 0.393528, 0.878321)84.07513, 20.51351, 37.9337
4given(0.519284, -0.523267, 0.675675), (-0.537358, -0.814704, -0.217954), (0.664523, -0.2499, -0.704244)-14.7012, -59.35347, -12.51783
5given(-0.511381, 0.537284, -0.670683), (-0.527323, -0.812432, -0.248767), (-0.678543, 0.226452, 0.698784)128.63203, -59.1803, 56.25545

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Components

#1: Protein
Tryparedoxin peroxidase


Mass: 24332.775 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: TRYP3, LMJF_15_1080 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QF76, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG 3350, 0.1 M BIS-TRIS PROPANE, 0.2 M KSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2011
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3→106 Å / Num. obs: 21162 / % possible obs: 99.9 % / Redundancy: 2.9 % / Rsym value: 0.15 / Net I/σ(I): 7.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.84 / Rsym value: 0.518 / % possible all: 99.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
MOLREPphasing
REFMAC5.6.0117refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2Y

1e2y


Resolution: 3→106 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / SU B: 14.645 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23342 1143 5.1 %RANDOM
Rwork0.19709 ---
obs0.19889 21162 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---1.29 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 3→106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 0 63 6547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196638
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9658982
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11524.144292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.668151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6651535
X-RAY DIFFRACTIONr_chiral_restr0.0850.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214983
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 93 -
Rwork0.296 1420 -
obs--99.08 %

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