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Open data
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Basic information
Entry | Database: PDB / ID: 7dkr | |||||||||
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Title | Crystal structure of native E. coli Grx2 at 2.38 A | |||||||||
![]() | Glutaredoxin | |||||||||
![]() | OXIDOREDUCTASE / E. coli Grx2 / Native | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sreekumar, S.N. / Arockiasamy, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of native E. coli Grx2 at 2.38 A Authors: Sreekumar, S.N. / Arockiasamy, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.7 KB | Display | ![]() |
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PDB format | ![]() | 37.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.5 KB | Display | ![]() |
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Full document | ![]() | 423.6 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kx4S 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 24383.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.9 % / Description: 2D Crystals |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, Reservoir condition:0.1M HEPES pH:7.5, 20% w/v PEG 10000, Protein/reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC ...Details: Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, Reservoir condition:0.1M HEPES pH:7.5, 20% w/v PEG 10000, Protein/reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with the drop size of 150 nl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→89.28 Å / Num. obs: 8647 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.036 / Rrim(I) all: 0.12 / Χ2: 0.92 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 877 / CC1/2: 0.973 / Rpim(I) all: 0.106 / Rrim(I) all: 0.332 / Χ2: 0.89 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4KX4 Resolution: 2.378→39.475 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.51 / 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: 73.34 Å2 / Biso mean: 18.5777 Å2 / Biso min: 5.96 Å2 | ||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.378→39.475 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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