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

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Basic information

Entry
Database: PDB / ID: 9hsu
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with cyanoacetamide
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
2-cyanoacetamide / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 cyanoacetamide
Authors: Audebert, S. / Gelin, M. / Guichou, J.-F.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 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)20,7312
Polymers20,6471
Non-polymers841
Water1,56787
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4624
Polymers41,2942
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1870 Å2
ΔGint-4 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.337, 70.327, 117.814
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-XHD / 2-cyanoacetamide


Mass: 84.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.52 Å3/Da / Density % sol: 51.29 %
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: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.861→60.39 Å / Num. obs: 27026 / % possible obs: 83.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.88 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.046 / Rrim(I) all: 0.092 / Net I/σ(I): 8.4
Reflection shellResolution: 1.861→1.988 Å / % possible obs: 23.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 1.004 / Num. measured all: 2543 / Num. unique obs: 747 / Rpim(I) all: 0.584 / Rrim(I) all: 1.174 / Net I/σ(I) obs: 1.4

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→60.39 Å / SU ML: 0.2541 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2548 1281 4.74 %
Rwork0.214 25745 -
obs0.216 27026 91.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.82 Å2
Refinement stepCycle: LAST / Resolution: 1.95→60.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 6 87 1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111086
X-RAY DIFFRACTIONf_angle_d0.97521469
X-RAY DIFFRACTIONf_chiral_restr0.0613170
X-RAY DIFFRACTIONf_plane_restr0.0084181
X-RAY DIFFRACTIONf_dihedral_angle_d14.2277395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.030.30021380.30822947X-RAY DIFFRACTION93.88
2.03-2.120.2911540.27572873X-RAY DIFFRACTION93.37
2.12-2.230.2791370.26162892X-RAY DIFFRACTION92.94
2.23-2.370.29291450.25742928X-RAY DIFFRACTION93.63
2.37-2.560.27191380.24322904X-RAY DIFFRACTION93.23
2.56-2.820.31111280.24472874X-RAY DIFFRACTION91.78
2.82-3.220.28181540.22822813X-RAY DIFFRACTION91.49
3.22-4.060.24791430.19682756X-RAY DIFFRACTION88.2
4.06-60.390.21471440.17322758X-RAY DIFFRACTION88.85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.26151095648-0.2603396750681.284154695654.00529237674-0.8467275024874.36475226995-0.0202668773789-0.1431770056970.1256806836410.103732049221-0.03820168147590.004650167215-0.101006032579-0.03431899210150.05080280113280.2223250987770.009464814684550.03907367776910.223496218811-0.02285572196110.238154057217-2.50816080503-22.3634239055-23.4212984562
28.71434279428-1.925636542732.912429043999.64300662524-0.05541631895012.75242877157-0.146887236852-0.8765139741920.1617358148630.956912313382-0.1634272094860.357139257907-0.0117285351425-0.4890347454930.2536188646970.354176951144-0.008488889061530.007759850645030.387495936995-0.07799713298820.31210265323-14.1729657696-15.0953459533-25.7243234067
39.08549669593-2.125731564755.47700338672.65577344-1.877789206083.625292864990.373051770853-1.042542223820.7363585987630.400613074842-0.051158444172-0.4746170036251.05467511644-1.53914646073-0.2815234353150.881232176583-0.1784982078230.1393472605380.631175448393-0.2047956541760.640066380222-8.18635766909-36.5195675186-6.93417237546
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 616 through 702 )616 - 7021 - 87
22chain 'A' and (resid 703 through 753 )703 - 75388 - 113
33chain 'A' and (resid 754 through 772 )754 - 772114 - 132

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