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- PDB-7zhx: Leishmania donovani Glucose 6-Phosphate Dehydrogenase (N-terminal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zhx | ||||||
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Title | Leishmania donovani Glucose 6-Phosphate Dehydrogenase (N-terminal deletion variant)complexed with NADP(H) | ||||||
![]() | Glucose-6-phosphate 1-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Trypanosoma / Leishmania donovani / Glucose 6-Phosphate Dehydrogenase / G6P / NADP(H) / pentose phosphate pathway | ||||||
Function / homology | ![]() glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fritz-Wolf, K. / Berneburg, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Leishmania donovani glucose 6-phosphate dehydrogenase reveals a unique N-terminal domain. Authors: Berneburg, I. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.8 KB | Display | ![]() |
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PDB format | ![]() | 91.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 916.8 KB | Display | ![]() |
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Full document | ![]() | 930.8 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zhtC ![]() 7zhuC ![]() 7zhvC ![]() 7zhwC ![]() 7zhyC ![]() 7zhzC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56793.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A2CIL3, glucose-6-phosphate dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 391 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NDP / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.55 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 6 % PEG 3000, 200 mM AmCl2 |
-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 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.3 Å / Num. obs: 58616 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 33.36 Å2 / CC1/2: 1 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.9→2 Å / Num. unique obs: 32174 / CC1/2: 0.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: D_1292122100 Resolution: 1.9→47.3 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9475 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 41.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→47.3 Å
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Refine LS restraints |
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LS refinement shell |
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