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

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Basic information

Entry
Database: PDB / ID: 9hsg
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with CDP-Choline
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
Chem-CDC / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 CDP-Choline
Authors: Audebert, S. / Guichou, J.-F. / Gelin, M.
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)21,1352
Polymers20,6471
Non-polymers4881
Water21612
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2714
Polymers41,2942
Non-polymers9772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area3870 Å2
ΔGint-18 kcal/mol
Surface area13830 Å2
Unit cell
Length a, b, c (Å)50.267, 70.805, 118.166
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-CDC / [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM


Mass: 488.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H26N4O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350 11.5%, NaF 210 nM, 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: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.08→31 Å / Num. obs: 22729 / % possible obs: 95.57 % / Redundancy: 3.8 % / Biso Wilson estimate: 55.82 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.15 / Net I/σ(I): 6.22
Reflection shellResolution: 2.08→2.2 Å / Num. unique obs: 3664 / CC1/2: 0.16

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→31 Å / SU ML: 0.4656 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 33.7029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2427 789 5.1 %
Rwork0.2251 14667 -
obs0.2261 15456 92.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.77 Å2
Refinement stepCycle: LAST / Resolution: 2.36→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 31 12 1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961161
X-RAY DIFFRACTIONf_angle_d0.95851587
X-RAY DIFFRACTIONf_chiral_restr0.0537184
X-RAY DIFFRACTIONf_plane_restr0.0059193
X-RAY DIFFRACTIONf_dihedral_angle_d17.407418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.510.39671390.36932537X-RAY DIFFRACTION95.1
2.51-2.70.36341330.32642488X-RAY DIFFRACTION94.59
2.7-2.970.29951260.33282460X-RAY DIFFRACTION92.85
2.97-3.40.32011280.25882434X-RAY DIFFRACTION91.57
3.4-4.280.22441340.19682427X-RAY DIFFRACTION91.43
4.29-310.17541290.16592321X-RAY DIFFRACTION87.56
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)
15.718184889671.12711272529-2.61232585775.9507556462-1.761911333383.53781028776-0.0117812195873-0.161825051622-0.2846615735610.718713649034-0.149091768937-0.1139426219320.1681569682380.2618341401090.1109803806570.5154865306310.0665648150657-0.09909695990180.421349697867-0.04145984629510.460770302284-20.1149385687-11.4561360946-25.1701530258
24.62284116492-0.11504097781-1.007215911394.366014943431.813739377944.31231317737-0.164242375902-0.218227009466-0.1890686466690.69620516409-0.121599724477-0.4415918987840.2695812369260.1006552169950.3057465761390.459105790090.014974200827-0.07352011193640.4216694515320.02462654203380.497085760827-20.9533097799-11.5804117234-21.4272197066
34.37640698109-0.471397981094-2.348197579729.366602269170.9698226746432.54068352878-0.516894050933-0.2799525007340.610440811420.7101665761340.03081618819970.6156366749640.555925097321-0.7467383290960.4113176730480.705017111961-0.140332029351-0.04337789145820.624822086102-0.05943659968840.452096179418-31.1939949317-7.92740893306-20.0668393839
44.60023494781-1.23223922977-1.421573402575.92001261518-0.1727897912892.65388018305-0.0676271604710.337370909448-0.603099774780.188127218141-0.325216186709-0.1694260851990.2235191514890.08355245721610.408525783950.4464125305740.0178874060275-0.02694577078160.4875282868240.0005925841904280.613890419315-21.4452662557-17.7670077619-28.0760022288
59.7874192341-2.931974028451.66806616623.358652838853.412452667986.73200403863-0.842989286825-0.57816821328-0.03511549223110.2368123561920.177226242796-0.1005415131860.8734206083840.1642080568860.5788917448140.937271930325-0.0804637025798-0.1895788789730.721126549380.1612058047390.678771657314-11.9396981284-23.2112623504-16.4974183866
61.6708387287-0.08983908080880.06272671672256.662071292673.871087050214.92607938204-0.3233343482530.158680229169-0.006369652944420.5113322945870.0447247267787-0.3115385787560.08537112221910.6735879939930.1189459382610.542157190187-0.0372256470191-0.1623441995850.5752825037220.1347481249770.83454666904-10.5143867249-14.7387782654-22.7909387397
75.038123089252.234791834020.2141443375213.54111819253-2.423244235912.49874049323-0.0509584847727-1.32622751087-0.2260131500791.2620322079-0.879743674650.610002528349-2.913296186991.720012859880.9236970935171.54256061663-0.379216510929-0.1432824601460.723468501580.221369741560.839143144598-19.5354676774.14395754826-3.05136998112
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 615 through 630 )615 - 6301 - 16
22chain 'A' and (resid 631 through 669 )631 - 66917 - 55
33chain 'A' and (resid 670 through 679 )670 - 67956 - 65
44chain 'A' and (resid 680 through 710 )680 - 71066 - 96
55chain 'A' and (resid 711 through 741 )711 - 74197 - 109
66chain 'A' and (resid 742 through 760 )742 - 760110 - 128
77chain 'A' and (resid 761 through 772 )761 - 772129 - 140

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