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Yorodumi- PDB-6yjf: Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yjf | |||||||||
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Title | Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from PEGSmear at pH 6.5 | |||||||||
Components | Phosphoglycerate kinase | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / phosphoglycerate kinase / metabolic enzyme / kinase | |||||||||
Function / homology | Function and homology information phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding Similarity search - Function | |||||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | |||||||||
Authors | Hyvonen, M. / Brear, P. / Blaszczyk, B.K. | |||||||||
Citation | Journal: to be published Title: Phosphoglycerate Kinase as a potential target for antimalarial therapy Authors: King, L. / Brear, P. / Bourgard, C. / Cassiano, C. / Mota, D. / Blaszczyk, B.K. / Tomaz, K. / Khedim, M. / Furlan, M. / Ramos, P. / Andresen, E. / Tarczykowska, A. / Tiburcio, L. / Kurowska, ...Authors: King, L. / Brear, P. / Bourgard, C. / Cassiano, C. / Mota, D. / Blaszczyk, B.K. / Tomaz, K. / Khedim, M. / Furlan, M. / Ramos, P. / Andresen, E. / Tarczykowska, A. / Tiburcio, L. / Kurowska, A. / Sulskis, D. / Oliver, S. / Grotli, M. / Massirer, K. / Saphire, E. / Burmann, B. / Witkowski, B. / Costa, F. / Sunnerhagen, P. / Hyvonen, M. / Bilsland, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yjf.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yjf.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 6yjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/6yjf ftp://data.pdbj.org/pub/pdb/validation_reports/yj/6yjf | HTTPS FTP |
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-Related structure data
Related structure data | 6y3aSC 6yjeC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVC01_070025900, PVP01_0721000, PVT01_070026100 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1G4HAR7, phosphoglycerate kinase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-OTQ / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25 %v/v PEGSM, 0.1 M MES 6.5 pH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||
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: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→68.66 Å / Num. obs: 34744 / % possible obs: 91.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 38.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Net I/σ(I): 14.3 / Num. measured all: 448345 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y3A Resolution: 1.85→25.05 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.138
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Displacement parameters | Biso max: 125.09 Å2 / Biso mean: 45.79 Å2 / Biso min: 27.17 Å2
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Refinement step | Cycle: final / Resolution: 1.85→25.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
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