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- PDB-6zmu: Crystal structure of the germline-specific thioredoxin protein De... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zmu | ||||||||||||
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Title | Crystal structure of the germline-specific thioredoxin protein Deadhead (Thioredoxin-1) from Drospohila melanogaster, P43212 | ||||||||||||
![]() | Thioredoxin-1![]() | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Baginski, B. / Pluta, R. / Macias, M.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190 KB | Display | ![]() |
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PDB format | ![]() | 153.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6z7oC ![]() 1xwaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 12560.693 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.05 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate, pH 5.0, 3.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→77.43 Å / Num. obs: 43714 / % possible obs: 96.7 % / Redundancy: 10.8 % / CC1/2: 1 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.97→2.054 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2187 / CC1/2: 0.617 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1xwa Resolution: 1.95→77.43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.461 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.161 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→77.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.952→2.003 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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