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- PDB-2vup: Crystal structure of a type II tryparedoxin-dependant peroxidase ... -

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Basic information

Entry
Database: PDB / ID: 2vup
TitleCrystal structure of a type II tryparedoxin-dependant peroxidase from Trypanosoma brucei
ComponentsGLUTATHIONE PEROXIDASE-LIKE PROTEIN
KeywordsOXIDOREDUCTASE / PEROXIDASE / TRYPANOSOMA / TRYPANOTHIONE / DITHIOL-DEPENDANT PEROXIDASE
Function / homology
Function and homology information


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: 2.1 Å
AuthorsAlphey, M.S. / Konig, J. / Fairlamb, A.H.
CitationJournal: Biochem.J. / Year: 2008
Title: Structural and Mechanistic Insights Into Type II Trypanosomatid Tryparedoxin-Dependent Peroxidases.
Authors: Alphey, M.S. / Konig, J. / Fairlamb, A.H.
History
DepositionMay 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE PEROXIDASE-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,1391
Polymers21,1391
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.260, 32.700, 58.310
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLUTATHIONE PEROXIDASE-LIKE PROTEIN / TRYPAREDOXIN-DEPENDANT PEROXIDASE / TRYPANOTHIONE/TRYPAREDOXIN DEPENDENT PEROXIDASE 2


Mass: 21139.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: 427 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q869A6, glutathione peroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsKYOTO ENCYCLOPEDIA OF GENES AND GENOMES (KEGG) DATABASE. THE AUTHOR SUGGESTS THR78ASN A NATURAL VARIANT.

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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: 2.2 Å3/Da / Density % sol: 36.58 % / Description: NONE
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→58 Å / Num. obs: 9469 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.5
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 12.2 / % possible all: 78.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P5Q

2p5q


Resolution: 2.1→58.03 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.835 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL HIS-TAG AND RESIDUES 1,2,167- 169 WERE DISORDERED AND NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 456 4.88 %RANDOM
Rwork0.205 ---
obs0.208 9544 98.1 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.461 Å20 Å2-1.641 Å2
2---1.412 Å20 Å2
3----0.388 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 0 96 1391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221349
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9711826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9495169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07825.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87115240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.452152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021023
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.2629
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2927
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.213
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5911.5854
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03321337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0853567
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7114.5486
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 39
Rwork0.232 607

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