[English] 日本語
![](img/lk-miru.gif)
- PDB-6jwv: Crystal structure of Plasmodium falciparum HPPK-DHPS A437G with S... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6jwv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Plasmodium falciparum HPPK-DHPS A437G with STZ-DHP | ||||||
![]() | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase | ||||||
![]() | TRANSFERASE / TIM barrel / kinase | ||||||
Function / homology | ![]() 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / dihydropteroate synthase activity / folic acid biosynthetic process / mitochondrial envelope / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Crystal structure of Plasmodium falciparum HPPK-DHPS wild type with Pteroate | ||||||
![]() | Chitnumsub, P. / Jaruwat, A. / Yuthavong, Y. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The structure of Plasmodium falciparum hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase reveals the basis of sulfa resistance. Authors: Chitnumsub, P. / Jaruwat, A. / Talawanich, Y. / Noytanom, K. / Liwnaree, B. / Poen, S. / Yuthavong, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 250.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 195.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 60.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jwqSC ![]() 6jwrC ![]() 6jwsC ![]() 6jwtC ![]() 6jwuC ![]() 6jwwC ![]() 6jwxC ![]() 6jwyC ![]() 6jwzC ![]() 6kckC ![]() 6kclC ![]() 6kcmC 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: 85943.461 Da / Num. of mol.: 2 / Fragment: HPPK-DHPS / Mutation: A437G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PPPK-DHPS / Plasmid: pET29a / Production host: ![]() ![]() |
---|
-Non-polymers , 8 types, 327 molecules ![](data/chem/img/XTZ.gif)
![](data/chem/img/PH2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PH2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PH2 / | #4: Chemical | #5: Chemical | ChemComp-ATP / | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ACT / #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % / Mosaicity: 0.53 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: microbatch / pH: 9 Details: 0.1 M bicine buffer pH 9.0, 0.5-0.6 M Ca acetate and 20%w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 51879 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.045 / Χ2: 0.949 / Net I/σ(I): 16.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6JWQ Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.868 / SU B: 9.915 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.844 / ESU R Free: 0.351 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120 Å2 / Biso mean: 46.656 Å2 / Biso min: 4.29 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.705→2.774 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|