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Open data
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Basic information
Entry | Database: PDB / ID: 3c1r | ||||||
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Title | Crystal structure of oxidized GRX1 | ||||||
![]() | Glutaredoxin-1![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yu, J. / Zhou, C.Z. | ||||||
![]() | ![]() Title: Glutathionylation-triggered conformational changes of glutaredoxin Grx1 from the yeast Saccharomyces cerevisiae. Authors: Yu, J. / Zhang, N.N. / Yin, P.D. / Cui, P.X. / Zhou, C.Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38 KB | Display | ![]() |
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PDB format | ![]() | 24.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3c1sC ![]() 2flsS 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: 13411.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: S288C / Gene: GRX1 / Plasmid: PET28B / Production host: ![]() ![]() ![]() References: UniProt: P25373, arsenate reductase (glutathione/glutaredoxin) |
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#2: Chemical | ChemComp-MES / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.41 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 20000, 0.1M MES, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→28.11 Å / Num. obs: 7126 / % possible obs: 95.3 % / Observed criterion σ(I): 1 / Redundancy: 4.05 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.12 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 5.2 / Num. unique all: 632 / % possible all: 90.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2FLS Resolution: 2→28.11 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 616709.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.67 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→28.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 10
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Xplor file |
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