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

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Basic information

Entry
Database: PDB / ID: 9hst
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with piperazin-2-one
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
piperazin-2-one / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 piperazin-2-one
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

Downloads & links

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Assembly

Deposited unit
A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7472
Polymers20,6471
Non-polymers1001
Water28816
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4944
Polymers41,2942
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1930 Å2
ΔGint-5 kcal/mol
Surface area14110 Å2
Unit cell
Length a, b, c (Å)50.480, 69.940, 118.565
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-XJJ / piperazin-2-one


Mass: 100.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
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-3 / Wavelength: 0.96577 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96577 Å / Relative weight: 1
ReflectionResolution: 2.39→60.24 Å / Num. obs: 16062 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 60.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.039 / Rrim(I) all: 0.119 / Χ2: 0.99 / Net I/σ(I): 13.1
Reflection shellResolution: 2.39→2.48 Å / % possible obs: 99.6 % / Redundancy: 9.5 % / Rmerge(I) obs: 2.178 / Num. measured all: 8354 / Num. unique obs: 880 / CC1/2: 0.516 / Rpim(I) all: 0.745 / Rrim(I) all: 2.304 / Χ2: 0.84 / Net I/σ(I) obs: 1

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→60.24 Å / SU ML: 0.5009 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.7163
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2512 801 4.99 %
Rwork0.2229 15261 -
obs0.2246 16062 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.29 Å2
Refinement stepCycle: LAST / Resolution: 2.39→60.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 7 16 1064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851069
X-RAY DIFFRACTIONf_angle_d0.8261450
X-RAY DIFFRACTIONf_chiral_restr0.0518168
X-RAY DIFFRACTIONf_plane_restr0.0084180
X-RAY DIFFRACTIONf_dihedral_angle_d16.0949382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.540.3651090.39172559X-RAY DIFFRACTION99.59
2.54-2.740.41521180.32682565X-RAY DIFFRACTION100
2.74-3.010.37041540.32142526X-RAY DIFFRACTION99.89
3.01-3.440.28581150.25172551X-RAY DIFFRACTION99.85
3.45-4.340.21841530.19522525X-RAY DIFFRACTION99.7
4.35-60.240.21161520.17382535X-RAY DIFFRACTION99.85
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)
17.88167961462-1.963068297955.115837031366.69430865661-5.38130752798.546998518590.219028973416-0.3991258945020.0233112353330.0849834457513-0.362232274561-0.2078929531680.3229123628040.3418227009270.00281264933170.452636515543-0.01022723503960.07067629602650.410131477754-0.06657991586820.438878326366-4.92806985175-23.5516824106-24.6084532573
26.46652584617-0.4773250021081.330802581824.73598466024-1.454675186673.24260713278-3.2258921655E-5-0.2732962509980.2241023210740.231374688064-0.0777069328550.2074022716520.04336778703030.1579950691160.07412407102150.323979920489-0.006452169801280.08275088735690.334947058365-0.02998489019150.334098870268-1.80498158125-24.7355383758-22.0786411282
35.682977669210.5579548608246.456743068235.920983337443.05415353498.51203228503-0.231784945404-0.2383290872420.276179336807-0.0366986857287-0.174055597316-0.253892349928-0.114982615488-0.6488975678250.4181505933180.6442495303540.03629354115410.0008435968430730.507551410177-0.01003258076580.574111228695-5.28162158337-13.2137705317-27.454240802
42.02395780842-1.566053295320.4949859860458.68532017429-0.5239155923072.00499454267-0.388005426469-1.50829574610.8472082365420.972712975624-0.749975558133-0.752191796298-0.535763941065-0.398502144911.03159294740.689367385933-0.0970402169992-0.04236341464580.840723995148-0.04915487548550.938242643037-16.3718194302-11.020158397-23.4727439928
57.99773521489-0.324850638050.2058616345436.752361384751.170328156544.165655964980.116014979051-1.32020784639-0.7116102060010.810033868587-0.4046351436660.6368201165350.655720312401-0.1252459044840.3230740863180.713723989085-0.006556713442050.1589957351120.748898457004-0.01783059790210.557710345995-14.6386109887-23.9250057063-22.2830119321
68.558619366192.45533599848-2.701386786340.928825923520.3844954386947.822927249820.247469569596-1.005463883350.445680742588-0.254941922028-0.09773219732661.641859353232.52654652532-1.14511438541-0.1065437532511.06216586161-0.3043351990410.05579544708641.12365911585-0.1899995514770.682469174895-5.3749615716-40.4639646802-1.04077939848
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 630 )616 - 6301 - 15
22chain 'A' and (resid 631 through 687 )631 - 68716 - 72
33chain 'A' and (resid 688 through 710 )688 - 71073 - 95
44chain 'A' and (resid 711 through 746 )711 - 74696 - 104
55chain 'A' and (resid 747 through 760 )747 - 760105 - 118
66chain 'A' and (resid 761 through 774 )761 - 774119 - 132

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