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- PDB-7dit: Structure of PfGrx1 in the intermediate state with cadmium and cesium -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dit | ||||||
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Title | Structure of PfGrx1 in the intermediate state with cadmium and cesium | ||||||
![]() | Glutaredoxin | ||||||
![]() | OXIDOREDUCTASE / REDOX ENZYME / TRX FOLD / GLUTATHIONE / Cd-SAD / CSO / S-HYDROXYCYSTEINE | ||||||
Function / homology | ![]() protein-disulfide reductase (glutathione) activity / Interconversion of nucleotide di- and triphosphates / glutathione disulfide oxidoreductase activity / antioxidant activity / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Manickam, Y. / Sharma, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Interaction of metals with PfGrx1 Authors: Manickam, Y. / Sharma, 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 | ![]() | 62.5 KB | Display | ![]() |
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PDB format | ![]() | 47.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dikC ![]() 7dilC ![]() 7dimC ![]() 7dinC ![]() 7dioC ![]() 7dipC ![]() 7diqC ![]() 7dirC ![]() 7disC ![]() 7diuC ![]() 7divC ![]() 7diwC ![]() 7dizC ![]() 7dj0C 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 12452.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate 3D7 / Gene: PF3D7_0306300 / Plasmid: PQE30 / Production host: ![]() ![]() References: UniProt: Q9NLB2, protein-disulfide reductase (glutathione) |
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-Non-polymers , 6 types, 139 molecules ![](data/chem/img/MPO.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MPO / | ||||||
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#3: Chemical | ChemComp-MPD / ( | ||||||
#4: Chemical | ChemComp-CD / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0.02 M amino acids, 0.1 M MOPS/HEPES sodium |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 4, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 10913 / % possible obs: 99.9 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.065 / Χ2: 1.357 / Net I/σ(I): 12.9 / Num. measured all: 158175 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 77.79 Å2 / Biso mean: 25.5247 Å2 / Biso min: 12.23 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→24.218 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -23.1399 Å / Origin y: 9.959 Å / Origin z: -4.8097 Å
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Refinement TLS group |
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