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

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Basic information

Entry
Database: PDB / ID: 9hsd
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 4-picolylamine
ComponentsCholinephosphate 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
1-(pyridin-4-yl)methanamine / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 4-picolylamine
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: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0263
Polymers20,8101
Non-polymers2162
Water82946
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0536
Polymers41,6202
Non-polymers4334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2160 Å2
ΔGint-10 kcal/mol
Surface area14610 Å2
Unit cell
Length a, b, c (Å)50.294, 67.901, 117.073
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 Cholinephosphate cytidylyltransferase


Mass: 20810.123 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: ctP, MAL13P1.86 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-NNW / 1-(pyridin-4-yl)methanamine


Mass: 108.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000 19%, TRIS pH8 0.1M 6-7-8-9-10% guanidine HCL 5-6-7% Glycerol

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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: Feb 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.817→58.737 Å / Num. obs: 19192 / % possible obs: 66.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 40.76 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.038 / Rrim(I) all: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 1.817→2.037 Å / % possible obs: 11.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.722 / Num. measured all: 1979 / Num. unique obs: 614 / Rpim(I) all: 0.466 / Rrim(I) all: 0.863 / Net I/σ(I) obs: 1.7

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→33.83 Å / SU ML: 0.2476 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235 998 5.2 %
Rwork0.2091 18194 -
obs0.2104 19192 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.74 Å2
Refinement stepCycle: LAST / Resolution: 2.18→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 16 46 1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711080
X-RAY DIFFRACTIONf_angle_d0.8141466
X-RAY DIFFRACTIONf_chiral_restr0.052171
X-RAY DIFFRACTIONf_plane_restr0.0094183
X-RAY DIFFRACTIONf_dihedral_angle_d14.2418377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.290.35261450.32372622X-RAY DIFFRACTION95.61
2.29-2.440.3111780.27942645X-RAY DIFFRACTION97.75
2.44-2.620.26471610.25212669X-RAY DIFFRACTION97.35
2.62-2.890.28671350.24562658X-RAY DIFFRACTION95.91
2.89-3.30.27641400.22332592X-RAY DIFFRACTION94.5
3.31-4.160.20691110.18572384X-RAY DIFFRACTION86.24
4.16-33.830.18241280.17142624X-RAY DIFFRACTION94.41
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)
13.62751150298-1.03461485668-0.5368750208816.293622205283.635760616662.441530639770.161686713659-0.06514534020360.06130103951470.1378412418620.00943243725027-0.2733583881830.328454856193-0.0869180854144-0.135903703130.5156599228830.0371032376682-0.02757707163950.2695870377170.04522285274880.255043097297-18.3079645138-8.18024375182-23.9273843017
25.70956437581-0.787435496968-1.410290660143.450822040081.040278333050.623842680811-0.169739393946-0.187381320986-0.3325743798940.2952067060070.02243896560050.03297056761490.374447816971-0.01143376464450.09535178976120.5322055187060.00626611886459-0.03307314469610.280304850410.01256946827010.221228124502-24.5452447989-12.9122812821-21.7546598749
34.17047097468-0.6547087865140.6516324917133.39266996645-3.52665534743.68240892241-0.0750847018835-0.192758545687-0.3230204969570.456510917993-0.0505636278058-0.1195032276690.2469930869360.1288298358370.1595710668160.6260541981910.05315687542020.03935115254220.342149845256-0.05824977890110.331627899707-13.3045274625-21.5360574594-28.389183671
47.87945226852-7.22632958153-8.610364542426.661206426447.815946366229.58357871169-0.736740909233-2.14388300530.2628361997510.3423568949620.9672825141570.5800276854560.6530831588382.12426726999-0.3109343736610.9001379199280.0654149028161-0.1065332801020.767640889268-0.097791390120.51873033075-11.974196731-4.41834120277-15.7350404276
57.73748042288-1.227205054141.222007989455.674333118351.745541207949.43059584518-0.468004051774-0.4805075086950.08913430413480.472675575403-0.379013074625-0.162122953907-1.460749160831.545147919090.8662149202260.7514186629-0.1764245928620.03781569583790.6906458513570.1067862550320.45082052882-19.20686734115.391131217340.376649468739
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 641 )615 - 6411 - 27
22chain 'A' and (resid 642 through 695 )642 - 69528 - 81
33chain 'A' and (resid 696 through 752 )696 - 75282 - 110
44chain 'A' and (resid 753 through 760 )753 - 760111 - 118
55chain 'A' and (resid 761 through 775 )761 - 775119 - 133

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