[English] 日本語
![](img/lk-miru.gif)
- PDB-5jo0: Structure of Plasmodium falciparum DXR in complex with a beta-sub... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5jo0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC56 and manganese | |||||||||
![]() | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | |||||||||
![]() | OXIDOREDUCTASE / ENZYME-INHIBITOR COMPLEX / MEP PATHWAY / ISOPRENOID BIOSYNTHESIS | |||||||||
Function / homology | ![]() apicoplast / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / NADPH binding / manganese ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 186.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 145.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 47.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jazSC ![]() 5jbiC ![]() 5jc1C ![]() 5jmpC ![]() 5jmwC ![]() 5jnlC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48164.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8IKG4, 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
---|
-Non-polymers , 6 types, 352 molecules ![](data/chem/img/L56.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/6LR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/6LR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-6LR / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% PEG 4000, 20% glycerol 0.1M MOPS/HEPES-Na pH 7.5 0.03M of each NPS (0.3M sodium nitrate, 0.3M disodium hydrogen phosphate, 0.3M ammonium sulfate) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94572 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.11 Å / Num. obs: 77884 / % possible obs: 95.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.7 / % possible all: 94.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5JAZ (lc51) Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.048 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.013 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|