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

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Basic information

Entry
Database: PDB / ID: 9hsj
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with piperidin-3-ol
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
: / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 piperidin-3-ol
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)20,8493
Polymers20,6471
Non-polymers2022
Water2,558142
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6986
Polymers41,2942
Non-polymers4054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2200 Å2
ΔGint-9 kcal/mol
Surface area14280 Å2
Unit cell
Length a, b, c (Å)50.392, 69.051, 118.892
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
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-A1IWV / (3~{R})-piperidin-3-ol


Mass: 101.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO / 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: 2.5 Å3/Da / Density % sol: 50.89 %
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: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.71→59.71 Å / Num. obs: 37562 / % possible obs: 98.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.01 Å2 / CC1/2: 0.985 / Net I/σ(I): 11.9
Reflection shellResolution: 1.71→1.74 Å / Num. unique obs: 1127 / CC1/2: 0.264

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→59.71 Å / SU ML: 0.2272 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 1819 4.84 %
Rwork0.19 35743 -
obs0.191 37562 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.02 Å2
Refinement stepCycle: LAST / Resolution: 1.76→59.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 14 142 1206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751084
X-RAY DIFFRACTIONf_angle_d0.7681467
X-RAY DIFFRACTIONf_chiral_restr0.0553172
X-RAY DIFFRACTIONf_plane_restr0.007179
X-RAY DIFFRACTIONf_dihedral_angle_d14.8756403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.34791270.31152836X-RAY DIFFRACTION96.77
1.81-1.860.33491270.29532828X-RAY DIFFRACTION95.76
1.86-1.920.29291320.28352802X-RAY DIFFRACTION96.01
1.92-1.990.24191660.23892681X-RAY DIFFRACTION93.25
1.99-2.070.29741390.2252817X-RAY DIFFRACTION97.14
2.07-2.160.22421310.19822814X-RAY DIFFRACTION96.27
2.16-2.280.23931300.19752798X-RAY DIFFRACTION95.1
2.28-2.420.21461310.20922676X-RAY DIFFRACTION92.18
2.42-2.610.22881360.18952788X-RAY DIFFRACTION95.71
2.61-2.870.21551510.2012711X-RAY DIFFRACTION93.71
2.87-3.280.1651480.17882693X-RAY DIFFRACTION92.24
3.29-4.140.17831700.15562636X-RAY DIFFRACTION92.45
4.14-59.710.19631310.16312663X-RAY DIFFRACTION90.48
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)
14.50629928165-1.245950376462.843421877444.07217888618-3.228799832246.33267297332-0.01192237940460.2090395616660.143600972546-0.0903739545428-0.136601044320.04889594524130.2352785689470.09126764636190.1631415806520.1597299817530.01739788887550.03699219616190.16701471748-0.02204686181220.18546502893-5.20606854292-23.2453543541-24.4268871088
28.93598235873-2.461167249574.455568822178.22971765121-4.908551727154.02207023862-0.00586898646597-0.613541413921-0.09521976558930.4821975790490.3169889656030.711609453398-0.0209791063404-0.83491393288-0.3068723600860.1798977927170.02053541558780.038798180620.222150007034-0.009546224372360.263763329092-8.97841435902-30.2419899741-23.2001462674
32.73712404622-0.2266318097631.234604510112.52609916744-0.1073299256522.86550736253-0.0602575213024-0.03613261771970.2156296416360.1743284822390.000452945889572-0.0726990290571-0.2284506628990.0986289753740.0711825565210.198733068261-0.008152292408870.023582751510.1858468136440.008281564916810.213366928678-0.519798577391-21.2955534346-21.428834166
49.490151423520.2874138789621.287957108919.716797902032.825907354043.67377306730.0446711571559-0.09892940035510.6072858418560.270407789174-0.0942870040134-0.0970899671864-0.291248097808-0.0218161288942-0.001497405661390.2678208662440.0127006116492-0.02699505566560.2324506289010.05226388908040.264348211032-8.58777965905-12.7184649617-29.1567408729
55.02461687940.2483469777363.189468990164.76352300671-0.4514806097175.03799350481-0.118476154757-0.1502951010880.4268135187580.112974565525-0.06167837599340.0237296415736-0.340278241935-0.0753146174549-0.09939102877760.2183993310460.02969295274170.03170394129050.304516915591-0.0304696456530.334047750612-16.9115445448-12.54472812-27.9063706884
62.37994749566-2.170495257981.329952007217.95604278282-4.876450313355.303512447290.1688228029820.2361290574910.0532065355696-0.004111779945550.07519242041540.2241189406810.0502113435316-0.496224525757-0.3143903533040.283532568164-0.02213084664770.06136492585810.329850996531-0.007981817973460.209244494918-7.68119216964-37.4249005453-5.56416350668
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 630 )616 - 6301 - 15
22chain 'A' and (resid 631 through 641 )631 - 64116 - 26
33chain 'A' and (resid 642 through 695 )642 - 69527 - 80
44chain 'A' and (resid 696 through 741 )696 - 74181 - 98
55chain 'A' and (resid 742 through 752 )742 - 75299 - 109
66chain 'A' and (resid 753 through 774 )753 - 774110 - 131

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