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- PDB-6yxt: Crystal structure of the ADP-bound form of choline kinase from Pl... -

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Basic information

Entry
Database: PDB / ID: 6yxt
TitleCrystal structure of the ADP-bound form of choline kinase from Plasmodium falciparum
ComponentsCholine kinase
KeywordsTRANSFERASE / choline kinase / ADP / complex
Function / homology
Function and homology information


Synthesis of PE / choline kinase / ethanolamine kinase activity / choline kinase activity / Synthesis of PC / phosphatidylethanolamine biosynthetic process / phosphatidylcholine biosynthetic process / choline binding / nucleotide binding / metal ion binding ...Synthesis of PE / choline kinase / ethanolamine kinase activity / choline kinase activity / Synthesis of PC / phosphatidylethanolamine biosynthetic process / phosphatidylcholine biosynthetic process / choline binding / nucleotide binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Choline/ethanolamine kinase / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Choline kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTorretta, A. / Parisini, E.
CitationJournal: Crystals / Year: 2020
Title: Crystal Structure of the Apo and the ADP-Bound Form of Choline Kinase from Plasmodium falciparum
Authors: Torretta, A. / Lopez-Cara, L.C. / Parisini, E.
History
DepositionMay 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9967
Polymers45,3341
Non-polymers6626
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-18 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.450, 68.000, 105.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Choline kinase


Mass: 45334.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1401800 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q8IM71, choline kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% (v/v) PEG 4000, 0.2 M NaCl, 0.1 M HEPES pH 7.5, 2 mM TCEP, 4 mM MgCl2 and 2 mM ADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→68 Å / Num. obs: 24873 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.994 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.32 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3571 / CC1/2: 0.486

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FI8

3fi8


Resolution: 2.2→56.17 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 1230 4.98 %
Rwork0.2305 23476 -
obs0.2318 24706 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.81 Å2 / Biso mean: 57.1555 Å2 / Biso min: 26.87 Å2
Refinement stepCycle: final / Resolution: 2.2→56.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 41 96 3152
Biso mean--50.23 54.66 -
Num. residues----359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.290.49921280.46042493262196
2.29-2.390.33951200.356225762696100
2.39-2.520.35821290.321425802709100
2.52-2.680.34171290.291625892718100
2.68-2.880.3231320.25526112743100
2.88-3.170.29491630.250725862749100
3.17-3.630.22091560.217525982754100
3.63-4.580.22151510.181726432794100
4.58-56.170.19791220.189528002922100

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