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- PDB-9hsh: Crystal structure of C-terminal catalytic domain of Plasmodium fa... -

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Basic information

Entry
Database: PDB / ID: 9hsh
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with Cytidine-triphosphate
Componentscholine-phosphate cytidylyltransferase
KeywordsTRANSFERASE / CCT
Function / homology
Function and homology information


Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / phosphatidylcholine binding / identical protein binding
Similarity search - Function
Choline-phosphate cytidylyltransferase Pcy1-like / CTP:phosphocholine cytidylyltransferase domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / : / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAudebert, S. / Gelin, M. / Guichou, J.-F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE44-0012 France
CitationJournal: To Be Published
Title: Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with Cytidine-triphosphate
Authors: Audebert, S. / Gelin, M. / Guichou, J.-F.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1853
Polymers20,6471
Non-polymers5382
Water1,49583
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3706
Polymers41,2942
Non-polymers1,0764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area3960 Å2
ΔGint-26 kcal/mol
Surface area13220 Å2
Unit cell
Length a, b, c (Å)50.494, 69.321, 117.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein choline-phosphate cytidylyltransferase


Mass: 20646.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Deletion of a lysine rich loop (720 - 737)
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1316600 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350 11.5%, NaF 210 mM, Glycerol 5.8%, MnCl2 15mM, 1,3 propandiol 3%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.8→59.64 Å / Num. obs: 29350 / % possible obs: 97.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.65 Å2 / CC1/2: 0.967 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 940 / CC1/2: 0.285

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→59.64 Å / SU ML: 0.3172 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.6948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.257 1418 4.83 %
Rwork0.2305 27932 -
obs0.2318 29350 79.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→59.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 30 83 1157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861124
X-RAY DIFFRACTIONf_angle_d0.87341535
X-RAY DIFFRACTIONf_chiral_restr0.0539177
X-RAY DIFFRACTIONf_plane_restr0.0063179
X-RAY DIFFRACTIONf_dihedral_angle_d25.88465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.443140.4685273X-RAY DIFFRACTION7.75
1.86-1.940.45991210.42132203X-RAY DIFFRACTION63.57
1.94-2.030.38331290.39133046X-RAY DIFFRACTION86.21
2.03-2.130.34591700.33233156X-RAY DIFFRACTION90.36
2.13-2.270.31521540.29353329X-RAY DIFFRACTION94.47
2.27-2.440.29731700.28293270X-RAY DIFFRACTION93.94
2.44-2.690.32111660.25433249X-RAY DIFFRACTION92.57
2.69-3.080.30751830.25623105X-RAY DIFFRACTION89.54
3.08-3.880.2411400.20593176X-RAY DIFFRACTION90.04
3.88-59.640.19061710.17573125X-RAY DIFFRACTION89.37

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