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- PDB-7py9: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7py9
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with (pyrrolidin-2-yl)methanol
ComponentsCholinephosphate cytidylyltransferase
KeywordsTRANSFERASE / Plasmodium Falciparum CCT Inhibitors Fragments
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
D-Prolinol / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsDuclovel, C. / Gelin, M. / Krimm, I. / Cerdan, R. / Guichou, J.-F.
Funding support France, 1items
OrganizationGrant numberCountry
Montpellier University of Excellence (MUSE) France
CitationJournal: To Be Published
Title: Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design of PfCCT inhibitors
Authors: Duclovel, C. / Gelin, M. / Wein, S. / Wengelnik, K. / Krimm, I. / Guichou, J.F. / Cerdan, R.
History
DepositionOct 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0123
Polymers20,8101
Non-polymers2022
Water64936
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0256
Polymers41,6202
Non-polymers4054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2280 Å2
ΔGint-7 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.254, 68.399, 118.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ctP, MAL13P1.86 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-8GZ / D-Prolinol / [(2~{R})-pyrrolidin-2-yl]methanol / [(2R)-pyrrolidin-2-yl]methanol / (pyrrolidin-2-yl)methanol / (2R)-pyrrolidin-2-ylmethanol


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.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8
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: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.89→46.26 Å / Num. obs: 31019 / % possible obs: 97.7 % / Redundancy: 2.725 % / Biso Wilson estimate: 49.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.054 / Χ2: 0.804 / Net I/σ(I): 10.79 / Num. measured all: 84529
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.89-22.7181.7820.5313491515149640.1842.18996.4
2-2.142.7060.8531.2112819480847380.5141.04898.5
2.14-2.312.6110.4192.411519448044120.790.51998.5
2.31-2.532.8480.2144.9911613413940770.9460.2698.5
2.53-2.832.8050.1188.6610290374036680.9850.14598.1
2.83-3.262.580.05516.688255328732000.9960.06897.4
3.26-3.992.8190.02930.537617276927020.9990.03597.6
3.99-5.632.7490.02338.145772217721000.9990.02896.5
5.63-46.262.7230.02341.143153119411580.9990.02897

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 2.03→46.26 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2102 1241 4.97 %
Rwork0.2022 23722 -
obs0.2027 24963 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.15 Å2 / Biso mean: 60.4732 Å2 / Biso min: 38.69 Å2
Refinement stepCycle: final / Resolution: 2.03→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 14 36 1124
Biso mean--63.75 56.03 -
Num. residues----131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.110.35291350.31482631276699
2.11-2.210.31351390.29052678281798
2.21-2.320.33691370.28762618275599
2.32-2.470.25361410.24032655279698
2.47-2.660.28641390.23972653279298
2.66-2.930.29961370.24072645278298
2.93-3.350.24461380.22682603274197
3.35-4.220.1931370.18062634277197
4.22-46.260.14351380.1622605274397
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)
15.5185-0.4175-0.37198.84561.57057.52760.01320.2463-0.23660.07010.0394-0.32540.316-0.0299-0.12910.20310.0462-0.07020.28040.00820.3411-19.5038-11.2622-25.4768
24.9715-0.5744-1.52387.81163.03982.1845-0.2914-0.43290.18820.3790.3192-1.0215-0.18160.3448-0.10450.48430.0457-0.05830.4190.03830.4893-16.1104-4.1673-23.2317
36.7464-0.453-0.44334.52680.66063.365-0.0599-0.0208-0.35910.22120.2030.23890.3918-0.33930.06780.33990.0164-0.03290.2507-0.04390.3836-21.3499-14.94-23.0999
46.6525-1.0408-1.41065.0064-0.3023.6707-0.1701-0.266-0.22840.3760.08150.19020.2215-0.16170.10750.3958-0.0254-0.02180.3503-0.0150.332-26.5944-12.0966-20.481
54.0296-2.53670.33275.606-4.39083.7060.0424-0.2652-0.58690.3617-0.3240.02060.22940.01260.1950.5220.02720.02110.434-0.02810.4844-13.2452-21.5823-28.3437
61.9707-6.5897-9.70859.10284.93789.5057-0.6413-1.13490.64671.82040.971-0.73441.72541.6667-0.64370.8371-0.0519-0.24430.87060.05560.9776-12.2087-4.0818-15.9657
77.1605-1.1364-5.05477.3076-1.42283.72220.0676-0.87190.17340.8443-0.0447-0.5059-0.43960.6079-0.03780.6558-0.0706-0.06920.73460.06020.4688-19.5355.7108-1.1394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 615 through 630 )A615 - 630
2X-RAY DIFFRACTION2chain 'A' and (resid 631 through 641 )A631 - 641
3X-RAY DIFFRACTION3chain 'A' and (resid 642 through 662 )A642 - 662
4X-RAY DIFFRACTION4chain 'A' and (resid 663 through 695 )A663 - 695
5X-RAY DIFFRACTION5chain 'A' and (resid 696 through 752 )A696 - 752
6X-RAY DIFFRACTION6chain 'A' and (resid 753 through 760 )A753 - 760
7X-RAY DIFFRACTION7chain 'A' and (resid 761 through 773 )A761 - 773

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