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- PDB-6jws: Crystal structure of Plasmodium falciparum HPPK-DHPS A437G with P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jws | ||||||
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Title | Crystal structure of Plasmodium falciparum HPPK-DHPS A437G with Pteroate | ||||||
![]() | 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 / 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 | ![]() | 264.5 KB | Display | ![]() |
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PDB format | ![]() | 207.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jwqSC ![]() 6jwrC ![]() 6jwtC ![]() 6jwuC ![]() 6jwvC ![]() 6jwwC ![]() 6jwxC ![]() 6jwyC ![]() 6jwzC ![]() 6kckC ![]() 6kclC ![]() 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: 85943.461 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: ![]() ![]() |
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-Non-polymers , 6 types, 493 molecules ![](data/chem/img/PT1.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/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 | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACT / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.9 % / Mosaicity: 0.593 ° |
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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: Mar 28, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→30 Å / Num. obs: 85609 / % possible obs: 99.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.042 / Χ2: 0.941 / Net I/σ(I): 17.9 / Num. measured all: 496348 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JWQ Resolution: 2.3→29.58 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.873 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120 Å2 / Biso mean: 36.645 Å2 / Biso min: 5.88 Å2
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Refinement step | Cycle: final / Resolution: 2.3→29.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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