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- PDB-6vpd: Crystal structure of Trgpx in apo form -

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Basic information

Entry
Database: PDB / ID: 6vpd
TitleCrystal structure of Trgpx in apo form
ComponentsGlutathione peroxidase
KeywordsOXIDOREDUCTASE / glutathione peroxidase
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin activity / cellular 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione peroxidase
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsAdriani, P.P. / De Oliveira, G.S. / Paiva, F.C.R. / Dias, M.V.B. / Chambergo, F.S.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development142311/2016-2 Brazil
Sao Paulo Research Foundation2017/25705-8 Brazil
Sao Paulo Research Foundation2014/24107-1 Brazil
Brazilian National Council for Scientific and Technological Development141090/2016-2 Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural and functional characterization of the glutathione peroxidase-like thioredoxin peroxidase from the fungus Trichoderma reesei.
Authors: Adriani, P.P. / de Paiva, F.C.R. / de Oliveira, G.S. / Leite, A.C. / Sanches, A.S. / Lopes, A.R. / Dias, M.V.B. / Chambergo, F.S.
History
DepositionFeb 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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: Glutathione peroxidase
B: Glutathione peroxidase


Theoretical massNumber of molelcules
Total (without water)44,3952
Polymers44,3952
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.128, 43.636, 103.498
Angle α, β, γ (deg.)90.000, 108.430, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Glutathione peroxidase


Mass: 22197.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain QM6a) (fungus)
Strain: QM6a / Gene: TRIREDRAFT_47136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0RHF8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 400, 200 mM magnesium chloride and 100 mM HEPES, pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→39.88 Å / Num. obs: 10842 / % possible obs: 99.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 43.52 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.087 / Rrim(I) all: 0.199 / Net I/σ(I): 7 / Num. measured all: 50721 / Scaling rejects: 100
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.746 / Num. measured all: 6150 / Num. unique obs: 1306 / CC1/2: 0.694 / Rpim(I) all: 0.372 / Rrim(I) all: 0.837 / Net I/σ(I) obs: 2.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cmi

3cmi


Resolution: 2.603→39.876 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.28
RfactorNum. reflection% reflection
Rfree0.2595 509 4.7 %
Rwork0.1941 --
obs0.1971 10840 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.33 Å2 / Biso mean: 47.2477 Å2 / Biso min: 25.14 Å2
Refinement stepCycle: final / Resolution: 2.603→39.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 0 14 2428
Biso mean---40.04 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092474
X-RAY DIFFRACTIONf_angle_d0.9863339
X-RAY DIFFRACTIONf_chiral_restr0.056354
X-RAY DIFFRACTIONf_plane_restr0.006427
X-RAY DIFFRACTIONf_dihedral_angle_d15.8831477
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6033-2.86520.32831270.223253699
2.8652-3.27960.32691230.21582586100
3.2796-4.13130.27261190.18642584100
4.1313-39.8760.21131400.1827262599

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