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- PDB-6fqz: Plasmodium falciparum 6-phosphogluconate dehydrogenase in its apo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fqz | |||||||||
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Title | Plasmodium falciparum 6-phosphogluconate dehydrogenase in its apo form, in complex with its cofactor NADP+ and in complex with its substrate 6-phosphogluconate | |||||||||
![]() | 6-phosphogluconate dehydrogenase, decarboxylating | |||||||||
![]() | OXIDOREDUCTASE / Plasmodium / complex / substrate / redox regulation | |||||||||
Function / homology | ![]() phosphogluconate 2-dehydrogenase activity / D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt, oxidative branch / pentose-phosphate shunt / NADP binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fritz-Wolf, K. / Haeussler, K. / Reichmann, M. / Rahlfs, S. / Becker, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of Plasmodium falciparum 6-Phosphogluconate Dehydrogenase as an Antimalarial Drug Target. Authors: Haeussler, K. / Fritz-Wolf, K. / Reichmann, M. / Rahlfs, S. / Becker, 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 | ![]() | 204.7 KB | Display | ![]() |
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PDB format | ![]() | 163.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 37.7 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fqxSC ![]() 6fqyC 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/6PG.gif)
![](data/chem/img/6PG.gif)
#1: Protein | Mass: 53055.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8IKT2, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) #2: Sugar | |
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-Non-polymers , 4 types, 297 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 6PG-Pf6PGD crystals were crystallized with 24% PEG 1500 and 20% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2017 |
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→49.41 Å / Num. obs: 82520 / % possible obs: 99.96 % / Redundancy: 10 % / Biso Wilson estimate: 38.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.053 / Rrim(I) all: 0.17 / Net I/σ(I): 10.28 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 0.68 / Num. unique obs: 8165 / CC1/2: 0.33 / Rpim(I) all: 0.99 / % possible all: 99.93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FQX Resolution: 1.9→49.409 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→49.409 Å
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Refine LS restraints |
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LS refinement shell |
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