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- PDB-8r2h: Cryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXP... -

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Basic information

Entry
Database: PDB / ID: 8r2h
TitleCryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Plasmodium falciparum
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / 1-deoxy-D-xylulose 5-phosphate synthase / thiamin di-phosphate complex / transketolase
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / chloroplast / membrane / metal ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsGawriljuk, V.O. / Godoy, A.S. / Oerlemans, R. / Groves, M.R.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission860816European Union
Medical Research Council (MRC, United Kingdom)218785/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Plasmodium falciparum
Authors: Gawriljuk, V.O. / Godoy, A.S. / Oerlemans, R. / Groves, M.R.
History
DepositionNov 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-deoxy-D-xylulose-5-phosphate synthase
B: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,8066
Polymers211,9072
Non-polymers8994
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11610 Å2
ΔGint-93 kcal/mol
Surface area50990 Å2
MethodPISA

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Components

#1: Protein 1-deoxy-D-xylulose-5-phosphate synthase


Mass: 105953.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: dxs / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O96694
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimer of 1-deoxy-D-xylulose 5-phosphate synthase with Thiamin diphosphate bound.
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 44.47 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1.2particle selection
4cryoSPARC4.1.2CTF correction
7PHENIX1.20.1-4487model fitting
9cryoSPARC4.1.2initial Euler assignment
10cryoSPARC4.1.2final Euler assignment
12Coot0.9.63D reconstruction
13PHENIX1.20.1-44873D reconstruction
14PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97205 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingAccession code: O96694 / Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE

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