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- PDB-6yje: Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yje | |||||||||
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Title | Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from PEG3350 and ammonium acetate at pH 5.5 | |||||||||
![]() | Phosphoglycerate kinase | |||||||||
![]() | BIOSYNTHETIC PROTEIN / phosphoglycerate kinase / metabolic enzyme / kinase | |||||||||
Function / homology | ![]() phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Blaszczyk, B.K. / Hyvonen, M. | |||||||||
![]() | ![]() Title: Phosphoglycerate Kinase as a potential target for antimalarial therapy Authors: Bilsland, E. / Costa, F. / Blaszczyk, B.K. / Hyvonen, M. / Sunnerhagen, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.1 KB | Display | ![]() |
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PDB format | ![]() | 75.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764.9 KB | Display | ![]() |
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Full document | ![]() | 764.9 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y3aSC ![]() 6yjfC 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
#1: Protein | Mass: 45199.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PVC01_070025900, PVP01_0721000, PVT01_070026100 / Plasmid: pHAT2 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-OTQ / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % / Mosaicity: 0.1 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M NH4 Acet, 25 % w/v PEG 3350, 0.1 M BIS-TRIS 5.5 pH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 5, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→68.01 Å / Num. obs: 54681 / % possible obs: 99.9 % / Redundancy: 20.1 % / Biso Wilson estimate: 33.06 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.02 / Rrim(I) all: 0.094 / Net I/σ(I): 16.9 / Num. measured all: 1099791 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Y3A Resolution: 1.62→23.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.097
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Displacement parameters | Biso max: 97.37 Å2 / Biso mean: 35.66 Å2 / Biso min: 19.89 Å2
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Refinement step | Cycle: final / Resolution: 1.62→23.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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