+Open data
-Basic information
Entry | Database: PDB / ID: 6z7o | ||||||
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Title | Crystal structure of Thioredoxin T from Drosophila melanogaster | ||||||
Components | Thioredoxin-T | ||||||
Keywords | NUCLEAR PROTEIN / Thioredoxin-T / Drosophila melanogaster / Oxidoreductase | ||||||
Function / homology | Function and homology information glycerol ether metabolic process / disulfide oxidoreductase activity / : / Y chromosome / protein-disulfide reductase activity / cell redox homeostasis / protein folding / oxidoreductase activity / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Freier, R. / Aragon, E. / Baginski, B. / Pluta, R. / Martin-Malpartida, P. / Torner, C. / Gonzaez, C. / Macias, M. | ||||||
Funding support | Spain, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z7o.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z7o.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 6z7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z7o_validation.pdf.gz | 414.7 KB | Display | wwPDB validaton report |
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Full document | 6z7o_full_validation.pdf.gz | 415.5 KB | Display | |
Data in XML | 6z7o_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 6z7o_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/6z7o ftp://data.pdbj.org/pub/pdb/validation_reports/z7/6z7o | HTTPS FTP |
-Related structure data
Related structure data | 6zmuC 1xwaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 15.0% w/v PEG 4000, 0.2 M potassium bromide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872899 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 3, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.872899 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.32 Å2 / Biso mean: 34.4913 Å2 / Biso min: 14.52 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.33→33.672 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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