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

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Basic information

Entry
Database: PDB / ID: 9hsn
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 1-cyclopropylmethanamine
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
cyclopropylmethanamine / BETA-MERCAPTOETHANOL / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 1-cyclopropylmethanamine
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)20,7963
Polymers20,6471
Non-polymers1492
Water1,29772
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5926
Polymers41,2942
Non-polymers2994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2500 Å2
ΔGint-10 kcal/mol
Surface area14280 Å2
Unit cell
Length a, b, c (Å)50.269, 69.000, 118.902
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-9L6 / cyclopropylmethanamine


Mass: 71.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
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: ID23-2 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 9M / 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: 1.9→46.301 Å / Num. obs: 21153 / % possible obs: 66.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 38.91 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.04 / Rrim(I) all: 0.084 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→2.088 Å / % possible obs: 13.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.904 / Num. measured all: 1976 / Num. unique obs: 560 / Rpim(I) all: 0.518 / Rrim(I) all: 1.05 / Net I/σ(I) obs: 1.5

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→46.3 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 1126 5.32 %
Rwork0.204 20027 -
obs0.2054 21153 89.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.19 Å2
Refinement stepCycle: LAST / Resolution: 2.09→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 9 72 1132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071080
X-RAY DIFFRACTIONf_angle_d0.76951462
X-RAY DIFFRACTIONf_chiral_restr0.0514171
X-RAY DIFFRACTIONf_plane_restr0.0046179
X-RAY DIFFRACTIONf_dihedral_angle_d13.7984390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.190.33881520.29282626X-RAY DIFFRACTION94.88
2.19-2.30.31741140.28022400X-RAY DIFFRACTION84.45
2.3-2.450.30061530.26292595X-RAY DIFFRACTION93.37
2.45-2.630.30751310.23692600X-RAY DIFFRACTION92.73
2.63-2.90.26041210.24582443X-RAY DIFFRACTION86.86
2.9-3.320.24471610.21252595X-RAY DIFFRACTION92.89
3.32-4.180.22181340.18152224X-RAY DIFFRACTION80.04
4.18-46.30.17161600.16232544X-RAY DIFFRACTION91.17
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)
15.244552494110.341011196661.192481793724.64890371594-0.2563161852373.0341673593-0.0607637055506-0.2236471025510.252658026550.2626115690810.03243839749530.0535173810108-0.2522760645570.008851433567890.009776161001630.2251543490820.02006047974680.03308870593080.211685855994-0.004657729421030.196232885654-2.53470336491-22.8515628384-22.2888442408
22.12318435564-1.29925259851-0.4186773913528.665240625951.746474858095.338507864610.179218057399-0.6963766753040.5794035867850.506205212492-0.3679748995790.0721434532744-0.648729670442-0.01192954736560.1275013566790.397665451061-0.00510387336673-0.09183400091510.381776798929-0.01719063549880.363451862768-11.4902402773-12.6992059817-28.6767920452
34.28200826629-4.252631301713.983309757889.38316058983-6.786616174156.519862910990.2091942014720.056138164801-0.116000663657-0.03445793308360.2012380411570.6223837267590.164661327866-0.889066769705-0.4367099298180.471551077298-0.01598393003970.03841336085120.565829428891-0.02605137340740.313918987647-7.49972334996-37.6710794907-5.18549761009
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 695 )616 - 6951 - 80
22chain 'A' and (resid 696 through 752 )696 - 75281 - 109
33chain 'A' and (resid 753 through 774 )753 - 774110 - 131

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