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Yorodumi- PDB-6kck: Crystal structure of Plasmodium falciparum HPPK-DHPS wild type wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kck | ||||||
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Title | Crystal structure of Plasmodium falciparum HPPK-DHPS wild type with pterin and p-hydroxybenzoate | ||||||
Components | 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase | ||||||
Keywords | TRANSFERASE / TIM barrel / kinase | ||||||
Function / homology | Function and homology information 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 | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Model details | Crystal structure of Plasmodium falciparum HPPK-DHPS wild type with Pteroate | ||||||
Authors | Chitnumsub, P. / Jaruwat, A. / Yuthavong, Y. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: Febs J. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kck.cif.gz | 254.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kck.ent.gz | 199.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kck ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kck | HTTPS FTP |
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-Related structure data
Related structure data | 6jwqC 6jwrSC 6jwsC 6jwtC 6jwuC 6jwvC 6jwwC 6jwxC 6jwyC 6jwzC 6kclC 6kcmC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 85957.492 Da / Num. of mol.: 2 / Fragment: HPPK-DHPS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PPPK-DHPS / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta(DE3)pLysS / References: UniProt: Q25704 |
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-Non-polymers , 8 types, 251 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % / Mosaicity: 0.582 ° |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.5→30 Å / Num. obs: 66864 / % possible obs: 97.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.019 / Rrim(I) all: 0.041 / Χ2: 0.845 / Net I/σ(I): 20.4 / Num. measured all: 308938 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JWR Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.508 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.268 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: 44.676 Å2 / Biso min: 7.66 Å2
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Refinement step | Cycle: final / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.553 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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