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Open data
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Basic information
Entry | Database: PDB / ID: 1i5g | ||||||
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Title | TRYPAREDOXIN II COMPLEXED WITH GLUTATHIONYLSPERMIDINE | ||||||
![]() | TRYPAREDOXIN II | ||||||
![]() | ELECTRON TRANSPORT / tryparedoxin | ||||||
Function / homology | ![]() protein-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. ...Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. / Flohe, L. / Hecht, H.-J. | ||||||
![]() | ![]() Title: Structures of tryparedoxins revealing interaction with trypanothione. Authors: Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. / Flohe, L. / Hecht, H.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51 KB | Display | ![]() |
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PDB format | ![]() | 34.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 625 KB | Display | ![]() |
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Full document | ![]() | 626.7 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ewxC ![]() 1ezkC ![]() 1fg4SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16223.512 Da / Num. of mol.: 1 / Mutation: C44S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-TS5 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.95 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: PEG 8000, Mes Tris glutathionylspermidine, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 25, 2000 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→28.87 Å / Num. all: 24911 / Num. obs: 24911 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.065 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 8.8 / Num. unique all: 3735 / Rsym value: 0.077 / % possible all: 92.1 |
Reflection | *PLUS Num. obs: 24680 / % possible obs: 89 % / Rmerge(I) obs: 0.065 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FG4 Resolution: 1.4→40.49 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 7 Å2
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Refine analyze | Luzzati coordinate error free: 0.075 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→40.49 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.176 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |