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- PDB-5jbi: 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: 5jbi | |||||||||
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Title | Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC52 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 | ![]() | 189.2 KB | Display | ![]() |
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PDB format | ![]() | 147.7 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 ![]() 5jc1C ![]() 5jmpC ![]() 5jmwC ![]() 5jnlC ![]() 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 Details: MATURE PROTEIN LACKS SIGNAL AND APICOPLAST TARGETING SEQUENCES Source: (gene. exp.) ![]() ![]() Gene: DXR, PF14_0641 / Organ: apicoplast / Plasmid: pEXP5-CT/TOPO / Production host: ![]() ![]() References: UniProt: Q8IKG4, 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
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-Non-polymers , 5 types, 478 molecules ![](data/chem/img/6J8.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: 2.42 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% PEG 8000, 20%ethylene glycol 0.1M MES/imidazole, pH 6.5 0.02M each alcohol: 1,6-hexanediol 1-butanol (RS)-1,2-propanediol 2-propanol 1,4-butanediol 1,3-propanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.78 Å / Num. obs: 95833 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.8 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JAZ Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.608 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.645 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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