+Open data
-Basic information
Entry | Database: PDB / ID: 7z4q | ||||||
---|---|---|---|---|---|---|---|
Title | Plasmodium falciparum pyruvate kinase mutant - C49A | ||||||
Components | Pyruvate kinase | ||||||
Keywords | TRANSFERASE / Redox regulation / glycolysis / malaria / drug-target | ||||||
Function / homology | Function and homology information Glycolysis / Neutrophil degranulation / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / protein homotetramerization / phosphorylation / magnesium ion binding ...Glycolysis / Neutrophil degranulation / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / protein homotetramerization / phosphorylation / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Dillenberger, M. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Structure / Year: 2022 Title: Prominent role of cysteine residues C49 and C343 in regulating Plasmodium falciparum pyruvate kinase activity. Authors: Dillenberger, M. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z4q.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z4q.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 7z4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/7z4q ftp://data.pdbj.org/pub/pdb/validation_reports/z4/7z4q | HTTPS FTP |
---|
-Related structure data
Related structure data | 7z4mC 7z4nC 7z4rC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 56769.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Plasmodium falciparum pyruvate kinase mutant - C49A Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_0626800 / Production host: Escherichia coli (E. coli) / References: UniProt: C6KTA4, pyruvate kinase |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM MES, pH 6.5, 50 mM KCl, 10 mM MgCl2 and 14-24% PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.2 Å / Num. obs: 153591 / % possible obs: 98.49 % / Redundancy: 4 % / Biso Wilson estimate: 59.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.67 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 4 % / Rmerge(I) obs: 1.185 / Num. unique obs: 15062 / CC1/2: 0.589 / % possible all: 97.96 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292121472 Resolution: 2.1→41.2 Å / SU ML: 0.3809 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.6874 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|