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- PDB-6kcl: Crystal structure of Plasmodium falciparum HPPK-DHPS A437G/K540E ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kcl | ||||||
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Title | Crystal structure of Plasmodium falciparum HPPK-DHPS A437G/K540E with pterin and p-hydroxybenzoate | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.9 KB | Display | ![]() |
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PDB format | ![]() | 192 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 58.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jwqC ![]() 6jwrSC ![]() 6jwsC ![]() 6jwtC ![]() 6jwuC ![]() 6jwvC ![]() 6jwwC ![]() 6jwxC ![]() 6jwyC ![]() 6jwzC ![]() 6kckC ![]() 6kcmC 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: 85943.398 Da / Num. of mol.: 2 / Fragment: HPPK-DHPS / Mutation: A437G, K540E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PPPK-DHPS / Plasmid: pET29a / Production host: ![]() ![]() |
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-Non-polymers , 8 types, 206 molecules ![](data/chem/img/PE0.gif)
![](data/chem/img/PHB.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PHB.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GOL.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 | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.68 % / Mosaicity: 0.396 ° |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→30 Å / Num. obs: 51949 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Rrim(I) all: 0.054 / Χ2: 0.913 / Net I/σ(I): 16.5 / Num. measured all: 323274 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JWR Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.776 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.571 / ESU R Free: 0.307 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: 50.471 Å2 / Biso min: 10.3 Å2
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Refinement step | Cycle: final / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.701→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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