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

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Basic information

Entry
Database: PDB / ID: 9hsl
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with isonicotinic acid
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
pyridine-4-carboxylic acid / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 isonicotinic acid
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)20,7702
Polymers20,6471
Non-polymers1231
Water1,11762
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5404
Polymers41,2942
Non-polymers2462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2050 Å2
ΔGint-6 kcal/mol
Surface area13880 Å2
Unit cell
Length a, b, c (Å)50.231, 70.112, 119.083
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-S3V / pyridine-4-carboxylic acid


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 51.56 %
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: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.15→60.42 Å / Num. obs: 22042 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 39.92 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.072 / Rrim(I) all: 0.179 / Χ2: 1.13 / Net I/σ(I): 7.9
Reflection shellResolution: 2.15→2.21 Å / % possible obs: 96.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 1.653 / Num. measured all: 6086 / Num. unique obs: 938 / CC1/2: 0.546 / Rpim(I) all: 0.7 / Rrim(I) all: 1.799 / Χ2: 1.06 / Net I/σ(I) obs: 1.3

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→60.42 Å / SU ML: 0.3783 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.6227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.292 1078 4.89 %
Rwork0.22 20964 -
obs0.2232 22042 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.3 Å2
Refinement stepCycle: LAST / Resolution: 2.15→60.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 9 62 1131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711090
X-RAY DIFFRACTIONf_angle_d0.78871475
X-RAY DIFFRACTIONf_chiral_restr0.0513170
X-RAY DIFFRACTIONf_plane_restr0.0052182
X-RAY DIFFRACTIONf_dihedral_angle_d6.4607143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.4211250.33372580X-RAY DIFFRACTION97.13
2.24-2.360.34711490.29832612X-RAY DIFFRACTION99.42
2.36-2.510.35071650.2742639X-RAY DIFFRACTION99.64
2.51-2.70.32081300.25322632X-RAY DIFFRACTION99.39
2.7-2.970.28881590.27382575X-RAY DIFFRACTION98.88
2.98-3.40.27621110.22052646X-RAY DIFFRACTION99.21
3.41-4.290.26271370.19472628X-RAY DIFFRACTION99.07
4.29-60.420.27711020.17552652X-RAY DIFFRACTION98.5
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)
15.10016067595-0.6127935580211.145645881334.13275038629-0.6816534924393.039519743970.0099735857927-0.0749124971430.1379989310770.163831867479-0.0836779373341-0.0299919023456-0.0583556211884-0.004004652141780.07007894163210.251046813676-0.0180666483840.04583083639040.336275421452-0.02740620574560.290148402773-2.44393858934-22.3043404031-23.4711105265
24.9069177407-3.512870305352.625393721237.18372916371-1.526655577491.41533881914-0.161997158519-0.634595506679-0.1025340006990.8397726753170.2236836186550.523241194064-0.16612218663-0.384986104119-0.02790925903420.413687819454-0.0072820262318-0.008218103095550.578960585264-0.09674056971060.447816461155-13.5945458304-18.3394185855-24.2004030992
36.001332733670.6406960663743.692702702161.443425349652.405824812075.23866700396-0.0659376227806-0.9772971888020.2436837449180.9857609112170.0527761074595-0.7552560470671.27349235013-1.088602386510.03423613020581.01329897458-0.2489474490080.07743859310190.782294486449-0.2167415264930.65884526305-5.28757385499-39.4383052059-2.66624298785
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 760 )703 - 76088 - 118
33chain 'A' and (resid 761 through 772 )761 - 772119 - 130

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