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Yorodumi- PDB-7zzi: Plasmodium falciparum hexokinase complexed with glucose and citrate -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zzi | ||||||
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Title | Plasmodium falciparum hexokinase complexed with glucose and citrate | ||||||
Components | Phosphotransferase | ||||||
Keywords | TRANSFERASE / glycolysis / hexokinase / phosphotransferase / actin-like ATPase | ||||||
Function / homology | Function and homology information hexokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / D-glucose binding / intracellular glucose homeostasis / glycolytic process / ATP binding Similarity search - Function | ||||||
Biological species | Plasmodium (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fritz-Wolf, K. / Dillenberger, M. / Rahlfs, S. / Becker, K. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structural Analysis of Plasmodium falciparum Hexokinase Provides Novel Information about Catalysis Due to a Plasmodium -Specific Insertion. Authors: Dillenberger, M. / Werner, A.D. / Velten, A.S. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zzi.cif.gz | 238.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zzi.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zzi_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7zzi_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7zzi_validation.xml.gz | 36.6 KB | Display | |
Data in CIF | 7zzi_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/7zzi ftp://data.pdbj.org/pub/pdb/validation_reports/zz/7zzi | HTTPS FTP |
-Related structure data
Related structure data | 6vygS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.993642826891, 0.077810745027, -0.0813598213216), (-0.0322578738098, -0.889176698113, -0.456425491302), (-0.107858064809, -0.450899420593, 0.886034057113)Vector: 140. ...NCS oper: (Code: given Matrix: (-0.993642826891, 0.077810745027, -0.0813598213216), Vector: |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 55330.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium (eukaryote) / Strain: isolate NF54 / Gene: CK202_5141, PFNF54_05159 / Production host: Escherichia coli (E. coli) References: UniProt: W7JZC2, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Sugar | |
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-Non-polymers , 4 types, 31 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PGE / | #6: 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: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 200 mM sodium citrate, 0.1 mM sodium citrate buffer (pH 3.4-4.0), 10 mM glucose, 10 mM ATP, 5 mM DTT PH range: 3.4-4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.796→49.48 Å / Num. obs: 27459 / % possible obs: 99.67 % / Redundancy: 10.1 % / Biso Wilson estimate: 95.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1198 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.796→2.896 Å / Rmerge(I) obs: 3.411 / Num. unique obs: 2644 / CC1/2: 0.305 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VYG Resolution: 2.8→49.48 Å / SU ML: 0.5384 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6589 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 2.16061356931 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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