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

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Basic information

Entry
Database: PDB / ID: 9hsw
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 5-amino-1H-pyrazol-3(2H)-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
: / BETA-MERCAPTOETHANOL / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 5-amino-1H-pyrazol-3(2H)-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)20,8243
Polymers20,6471
Non-polymers1772
Water1,910106
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6486
Polymers41,2942
Non-polymers3544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2490 Å2
ΔGint-8 kcal/mol
Surface area13550 Å2
Unit cell
Length a, b, c (Å)50.178, 70.708, 118.435
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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-A1IWS / 5-azanyl-1,2-dihydropyrazol-3-one


Mass: 99.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
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: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.65→40.92 Å / Num. obs: 46253 / % possible obs: 94.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 38.19 Å2 / CC1/2: 0.999 / Net I/σ(I): 8.46
Reflection shellResolution: 1.65→1.75 Å / Num. unique obs: 5157 / CC1/2: 0.082

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→34.47 Å / SU ML: 0.2701 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 27.7487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2449 1740 4.56 %
Rwork0.2123 36383 -
obs0.2138 38123 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.61 Å2
Refinement stepCycle: LAST / Resolution: 1.76→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 11 106 1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681066
X-RAY DIFFRACTIONf_angle_d0.73321442
X-RAY DIFFRACTIONf_chiral_restr0.0544168
X-RAY DIFFRACTIONf_plane_restr0.006177
X-RAY DIFFRACTIONf_dihedral_angle_d12.6374382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.3351480.3643079X-RAY DIFFRACTION95.25
1.81-1.870.36111500.32143032X-RAY DIFFRACTION95.01
1.87-1.940.35831420.31163085X-RAY DIFFRACTION94.86
1.94-2.010.29661420.2863008X-RAY DIFFRACTION94.23
2.01-2.110.2891440.24863074X-RAY DIFFRACTION95.4
2.11-2.220.29181500.24263042X-RAY DIFFRACTION94.77
2.22-2.360.25351460.22863008X-RAY DIFFRACTION94.32
2.36-2.540.20541470.23163053X-RAY DIFFRACTION94.62
2.54-2.790.28631420.24173023X-RAY DIFFRACTION94.82
2.79-3.20.25581470.223051X-RAY DIFFRACTION94.17
3.2-4.030.24391400.18792991X-RAY DIFFRACTION93.74
4.03-34.470.19591420.1742937X-RAY DIFFRACTION90.88
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)
15.450757520210.484219296642.439058118714.00228925218-0.568695334094.82755760093-0.0176127372516-0.1900273197770.09118022005650.189302037276-0.04142108113950.0829566824804-0.0931849152204-0.03746623037940.07305843060330.2157878619350.02821645775260.04473618128230.270191497491-0.01739538509640.279470001354-5.16804875393-23.9864272379-23.7337615037
25.856454721580.2513194761562.443062374886.121531782490.4940004565012.14881154558-0.0302314842932-0.309747959083-0.02596420188440.173233906651-0.00102547271141-0.247473209221-0.0933924929457-0.02806366558370.05107135326560.307846631493-0.0189314694760.03780142457150.332075171360.03130676394720.2570899943911.62197544629-23.4315417856-20.9066860756
34.529038621763.94132243184-0.4153494091467.925552850180.49978735744.714622308240.04903909915650.1732983958790.473436432913-0.0329629570478-0.02755437904060.0672074923606-0.5301243942030.106596715138-0.01619479520270.3302290244890.0581463195531-0.02706820346210.3696022750250.03892533132190.40056563578-6.22163588814-13.2686716578-30.9453675906
48.94825217218-4.08200135256-1.806382818912.15887098756-0.7824798252619.05496074783-0.353688118002-1.786720303360.4625487934692.698829850430.4577129855010.235470567051-0.806387251696-0.26792664036-0.2946635195460.8638938510390.1409879835120.07300258786270.886210765629-0.09838764533410.665865120357-15.387960632-14.6033281034-18.9727987551
52.17011536276-1.919811925072.762662298315.46114199048-3.489457496224.54407631932-0.122516092448-0.6099078675390.0213854203250.7157120120450.223841951901-0.1578960066840.144424997021-0.656305242786-0.108762879850.52364461976-0.05791826030230.04544305122410.565607051213-0.07480424444470.438803297385-11.5259172883-27.0740122959-15.8311137299
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 662 )616 - 6621 - 47
22chain 'A' and (resid 663 through 695 )663 - 69548 - 80
33chain 'A' and (resid 696 through 709 )696 - 70981 - 94
44chain 'A' and (resid 710 through 741 )710 - 74195 - 100
55chain 'A' and (resid 742 through 772 )742 - 771101 - 130

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