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- PDB-6z7o: Crystal structure of Thioredoxin T from Drosophila melanogaster -

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Basic information

Entry
Database: PDB / ID: 6z7o
TitleCrystal structure of Thioredoxin T from Drosophila melanogaster
ComponentsThioredoxin-T
KeywordsNUCLEAR PROTEIN / Thioredoxin-T / Drosophila melanogaster / Oxidoreductase
Function / homology
Function and homology information


Y chromosome / protein-disulfide reductase activity / protein folding / nucleus
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsFreier, R. / Aragon, E. / Baginski, B. / Pluta, R. / Martin-Malpartida, P. / Torner, C. / Gonzaez, C. / Macias, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
European Union (EU)IRBPostPro2.0_600404 Spain
Citation
Journal: Iucrj / Year: 2021
Title: Structures of the germline-specific Deadhead and thioredoxin T proteins from Drosophila melanogaster reveal unique features among thioredoxins.
Authors: Freier, R. / Aragon, E. / Baginski, B. / Pluta, R. / Martin-Malpartida, P. / Ruiz, L. / Condeminas, M. / Gonzalez, C. / Macias, M.J.
#1: Journal: Biorxiv / Year: 2020
Title: Structures of the germline-specific Deadhead and Thioredoxin T proteins from Drosophila melanogaster reveal unique features among Thioredoxins
Authors: Freier, R. / Aragon, E. / Baginski, B. / Pluta, R. / Martin-Malpartida, P. / Ruiz, L. / Condeminas, M. / Gonzaez, C. / Macias, M.
History
DepositionMay 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6463
Polymers17,5151
Non-polymers1312
Water61334
1
A: Thioredoxin-T
hetero molecules

A: Thioredoxin-T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2936
Polymers35,0312
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Unit cell
Length a, b, c (Å)46.090, 49.312, 54.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thioredoxin-T / ThioredoxinT


Mass: 17515.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminus from 107 to 124 (GVYTDEAADVKAVHIDGE) and 129 to 157(LTAESSESDNDNNNVNEVSAHDENAVLEH) not modeled
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: TrxT, CG3315 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IFW4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 15.0% w/v PEG 4000, 0.2 M potassium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872899 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872899 Å / Relative weight: 1
ReflectionResolution: 2.32→35.08 Å / Num. obs: 6247 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 31.19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.079 / Rrim(I) all: 0.233 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.32-2.395.91.24423033900.6760.5211.3541.998.4
10.42-35.086.70.062566840.9960.0240.0671598.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1683refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XWA

1xwa


Resolution: 2.33→33.672 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 566 9.98 %
Rwork0.1917 5104 -
obs0.1947 5670 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.32 Å2 / Biso mean: 34.4913 Å2 / Biso min: 14.52 Å2
Refinement stepCycle: final / Resolution: 2.33→33.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 0 2 34 910
Biso mean--35.92 40.26 -
Num. residues----110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017890
X-RAY DIFFRACTIONf_angle_d1.51203
X-RAY DIFFRACTIONf_chiral_restr0.046141
X-RAY DIFFRACTIONf_plane_restr0.009154
X-RAY DIFFRACTIONf_dihedral_angle_d15.947329
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.33-2.55390.30211430.2719122599
2.5539-2.92320.31431340.22951255100
2.9232-3.68220.20041420.18531270100
3.6822-33.6720.18271470.16161354100

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