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- PDB-3dwv: Glutathione peroxidase-type tryparedoxin peroxidase, oxidized form -

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Basic information

Entry
Database: PDB / ID: 3dwv
TitleGlutathione peroxidase-type tryparedoxin peroxidase, oxidized form
ComponentsGlutathione peroxidase-like protein
KeywordsOXIDOREDUCTASE / alpha beta / 3-Layer(aba) Sandwich / Glutaredoxin fold / Peroxidase
Function / homology
Function and homology information


glycosome / glutathione peroxidase activity / response to oxidative stress
Similarity search - Function
Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione peroxidase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsTews, I. / Sinning, I. / Krauth-Siegel, L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for a distinct catalytic mechanism in Trypanosoma brucei tryparedoxin peroxidase.
Authors: Melchers, J. / Diechtierow, M. / Feher, K. / Sinning, I. / Tews, I. / Krauth-Siegel, R.L. / Muhle-Goll, C.
History
DepositionJul 23, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione peroxidase-like protein
B: Glutathione peroxidase-like protein


Theoretical massNumber of molelcules
Total (without water)41,9682
Polymers41,9682
Non-polymers00
Water6,485360
1
A: Glutathione peroxidase-like protein


Theoretical massNumber of molelcules
Total (without water)20,9841
Polymers20,9841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione peroxidase-like protein


Theoretical massNumber of molelcules
Total (without water)20,9841
Polymers20,9841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.810, 105.864, 42.738
Angle α, β, γ (deg.)90.000, 100.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione peroxidase-like protein / glutathione peroxidase Px III / Trypanothione/tryparedoxin dependent peroxidase 3


Mass: 20983.975 Da / Num. of mol.: 2 / Mutation: C76S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: gpx3, Tb927.7.1140 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q869A5, glutathione peroxidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE VARIATIONS AT THESE POSITIONS HAVE BEEN REPORTED IN REF. 1 OF UNIPROT (Q869A5_9TRYP).

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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: 2.22 Å3/Da / Density % sol: 45.79 % / Mosaicity: 0.403 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M ammonium sulphate, 0.1M sodium acetate, 1mM EDTA, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2006 / Details: torodial focusing mirrors
RadiationMonochromator: ESRF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. all: 71867 / Num. obs: 71308 / % possible obs: 99.2 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.001 / Net I/σ(I): 14.9
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2343 / Χ2: 1 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT3.006data extraction
DNAdata collection
HKL-2000data reduction
MOLREPphasing
ARP/wARPmodel building
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GS3

2gs3


Resolution: 1.41→30 Å / Num. parameters: 28282 / Num. restraintsaints: 37331 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1764 3516 5 %RANDOM
Rwork0.1157 ---
all0.128 71308 --
obs0.128 67756 94.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Displacement parametersBiso max: 77.08 Å2 / Biso mean: 18.568 Å2 / Biso min: 3.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.2642 Å20.1895 Å20.9485 Å2
2--0 Å2-0.1162 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.161 Å
Refinement stepCycle: LAST / Resolution: 1.41→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 0 360 2930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.069
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
1.41-1.460.245X-RAY DIFFRACTION6816
1.46-1.520.204X-RAY DIFFRACTION6833
1.52-1.590.175X-RAY DIFFRACTION6976
1.59-1.680.143X-RAY DIFFRACTION6805
1.68-1.780.119X-RAY DIFFRACTION6516
1.78-1.920.102X-RAY DIFFRACTION6721
1.92-2.110.096X-RAY DIFFRACTION6739
2.11-2.420.098X-RAY DIFFRACTION6886
2.42-3.050.104X-RAY DIFFRACTION6745
3.05-500.131X-RAY DIFFRACTION6719

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