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- PDB-5jnl: Structure of Plasmodium falciparum DXR in complex with a beta-sub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jnl | |||||||||
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Title | Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC54 and manganese | |||||||||
![]() | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | |||||||||
![]() | OXIDOREDUCTASE / ENZYME-INHIBITOR COMPLEX / MEP PATHWAY / ISOPRENOID BIOSYNTHESIS | |||||||||
Function / homology | ![]() 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / apicoplast / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / NADPH binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase with beta-Arylpropyl Analogues of Fosmidomycin. Authors: Sooriyaarachchi, S. / Chofor, R. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Dowd, C.S. / Maes, L. / Wouters, J. / Jones, T.A. / Van Calenbergh, S. / Mowbray, S.L. #1: ![]() Title: Synthesis and bioactivity of beta-substituted fosmidomycin analogues targeting 1-deoxy-D-xylulose-5-phosphate reductoisomerase. Authors: Chofor, R. / Sooriyaarachchi, S. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Johny, C. / Haymond, A. / Everaert, A. / Dowd, C.S. / Maes, L. / Coenye, T. / Alex, A. / Couch, R.D. / Jones, ...Authors: Chofor, R. / Sooriyaarachchi, S. / Risseeuw, M.D. / Bergfors, T. / Pouyez, J. / Johny, C. / Haymond, A. / Everaert, A. / Dowd, C.S. / Maes, L. / Coenye, T. / Alex, A. / Couch, R.D. / Jones, T.A. / Wouters, J. / Mowbray, S.L. / Van Calenbergh, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.1 KB | Display | ![]() |
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PDB format | ![]() | 149.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5jazSC ![]() 5jbiC ![]() 5jc1C ![]() 5jmpC ![]() 5jmwC ![]() 5jo0C 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 48164.477 Da / Num. of mol.: 2 / Fragment: UNP residues 75-488 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DXR, PF14_0641 / Organ: APICOPLAST / Plasmid: PEXP-5-CT/TOPO / Production host: ![]() ![]() References: UniProt: Q8IKG4, 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
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-Non-polymers , 5 types, 525 molecules ![](data/chem/img/L54.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: LC54 - E11 10% PEG 4000, 20% glycerol 0.1M bicine Trizma pH 8.5 0.03M of each ethylene glycol (0.3M diethyleneglycol, 0.3M triethyleneglycol, 0.3M tetraethyleneglycol, 0.3M pentaethyleneglycol) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.55 Å / Num. obs: 109929 / % possible obs: 94.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.6 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JAZ (LC51) Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.046 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.242 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→30 Å
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Refine LS restraints |
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