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

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Basic information

Entry
Database: PDB / ID: 9hsi
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with Phosphocholine
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
PHOSPHOCHOLINE / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 Phosphocholine
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)20,8312
Polymers20,6471
Non-polymers1841
Water2,558142
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6624
Polymers41,2942
Non-polymers3682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area3010 Å2
ΔGint5 kcal/mol
Surface area13890 Å2
Unit cell
Length a, b, c (Å)50.275, 70.256, 118.203
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-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 51.34 %
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: 0.8731 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: 1.77→60.39 Å / Num. obs: 28356 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.01 Å2 / CC1/2: 0.681 / Net I/σ(I): 6.5
Reflection shellResolution: 1.77→1.8 Å / Num. unique obs: 1042 / CC1/2: 0.29

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→60.39 Å / SU ML: 0.2743 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.5696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2338 1401 4.94 %
Rwork0.2003 26955 -
obs0.2019 28356 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.63 Å2
Refinement stepCycle: LAST / Resolution: 1.97→60.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 11 142 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911093
X-RAY DIFFRACTIONf_angle_d0.87691484
X-RAY DIFFRACTIONf_chiral_restr0.0518171
X-RAY DIFFRACTIONf_plane_restr0.0086182
X-RAY DIFFRACTIONf_dihedral_angle_d16.6753399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.040.31891240.28912733X-RAY DIFFRACTION99.1
2.04-2.120.29911320.2542631X-RAY DIFFRACTION97.02
2.12-2.220.26481570.25482679X-RAY DIFFRACTION98.17
2.22-2.340.28391400.23132693X-RAY DIFFRACTION99.89
2.34-2.480.26721170.22872721X-RAY DIFFRACTION99.89
2.48-2.670.31341590.21762698X-RAY DIFFRACTION100
2.67-2.940.25031420.22112709X-RAY DIFFRACTION98.92
2.94-3.370.22731320.19522654X-RAY DIFFRACTION97.79
3.37-4.240.16911470.16662731X-RAY DIFFRACTION99.93
4.24-60.390.21981510.172706X-RAY DIFFRACTION99.62
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)
16.09536223114-0.0703665814509-3.193545492585.048334217091.534966994624.704612563720.116235439803-0.01358450162340.06820063662890.02429762283610.00314252434005-0.182607292058-0.1164967418130.0212668696101-0.1106898263860.1411059883130.0102660443328-0.02834366532080.1553986089370.02693983928540.206268805878-18.3733256873-9.1318304853-26.7908216336
26.31677297831-6.750748718521.03915963347.25633696206-0.622768874145.69650022357-0.257258169629-0.979820701659-0.6638026990410.39227272113-0.01003194615720.2287563604750.85477650262-0.2108299902970.2495778099420.3049384285880.003399202947360.03776215211330.325353289360.09950239320730.317152045909-26.4816865247-17.4979576502-11.0778142776
34.604874950370.261017538107-1.346617608646.37560818909-0.7663490798562.921684865790.0531902235246-0.06036198261330.1339655599550.1825359968820.009083964451130.141108317176-0.0567628226255-0.157112293412-0.05684028879960.157123108902-0.0246289842206-0.04161632197760.176850299876-0.01555996512160.167624839516-26.8927302827-11.6187330697-23.3176003017
48.26894413822-1.010730287961.540577140960.970670884403-0.7449294349123.06826827102-0.133583963056-0.368518382721-0.5742228867140.327957700870.002170013571680.008248100400480.0745136617696-0.0372614723780.1092786115180.3160633774640.02381076355090.0380991837920.2159739296420.02570376297320.311697965457-14.6144810522-22.3675930911-27.3559811683
58.31805119755-7.03152619672-7.751214775658.904284153097.544701450259.29445558367-0.208804269745-1.143375235140.4202349216771.136727177180.828893022568-0.442953467280.491568128871.05522079045-0.5689835367220.3894620406820.0219003391314-0.047742657680.4784788032430.04745114639580.379882472099-11.2044817739-10.1781361343-20.9833109451
64.472584962980.703746846450.3276559333334.14909926509-1.096664362110.859748875938-0.466518861849-0.120691700573-0.583460191325-0.2426728020130.6133229404830.4626035094090.08835676862880.389655407239-0.4483426477240.686673778046-0.162670650986-0.08895464418420.4550452698260.2119252690750.251172417292-19.45122800025.14424367684-1.64510908035
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 653 )616 - 6531 - 38
22chain 'A' and (resid 654 through 669 )654 - 66939 - 54
33chain 'A' and (resid 670 through 695 )670 - 69555 - 80
44chain 'A' and (resid 696 through 747 )696 - 74781 - 105
55chain 'A' and (resid 748 through 760 )748 - 760106 - 118
66chain 'A' and (resid 761 through 774 )761 - 774119 - 132

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