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- PDB-7q2k: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7q2k
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-pyrrolidinone
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
pyrrolidin-2-one / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 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)20,8952
Polymers20,8101
Non-polymers851
Water1,09961
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7904
Polymers41,6202
Non-polymers1702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)50.429, 68.393, 116.836
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 BL21(DE3) (bacteria)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-BAQ / pyrrolidin-2-one / 2-Pyrrolidone


Mass: 85.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8
Details: PEG 4000 19%, TRIS pH8 0.1M Guanidine HCl 6-7-8-9-10% Glycerol 5-6-7%

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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: 1.653→40.588 Å / Num. obs: 15233 / % possible obs: 91.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 38.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.02 / Rrim(I) all: 0.043 / Net I/σ(I): 18.6 / Num. measured all: 74158
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.653-1.8395.30.93544168300.6620.4421.0381.651
5.255-40.5884.10.02534038290.9930.0150.02954.197.4

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Processing

Software
NameVersionClassification
PHENIXv1.19refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 1.94→40.59 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 1363 4.92 %
Rwork0.1977 26347 -
obs0.1993 15220 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.4 Å2 / Biso mean: 47.1827 Å2 / Biso min: 28.9 Å2
Refinement stepCycle: final / Resolution: 1.94→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 13 61 1162
Biso mean--55.89 47.65 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-2.010.38551290.32832568269793
2.01-2.090.31941440.28912636278098
2.09-2.180.32121400.26462740288099
2.18-2.30.28031290.23692706283598
2.3-2.440.2661410.24142662280398
2.44-2.630.23951320.21022685281797
2.63-2.90.2621410.23092558269992
2.9-3.320.24051500.20592608275896
3.32-4.180.19371460.17242596274295
4.18-40.590.19051110.15862588269993
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)
13.8813-0.392-0.54744.5080.10532.70670.05580.0727-0.0073-0.2391-0.0464-0.32660.15270.17820.0150.32480.0242-0.00090.30320.02670.3093-18.0814-8.1787-24.3577
23.9372-0.7083-0.61323.8805-0.11282.3151-0.1229-0.0311-0.3340.11630.07380.10180.4112-0.10780.05650.3042-0.0076-0.02780.2415-0.02260.2768-24.1586-12.9051-21.3749
32.6810.3672-0.94475.2875-1.62380.3373-0.1852-0.5904-0.0961-0.0093-0.2045-0.34360.0118-0.04520.32370.49050.06260.04080.4356-0.0440.3985-12.8913-21.3102-27.9747
49.0537-0.9323.06479.3229-1.81261.316-0.0042-0.3118-0.35790.01190.168-0.79350.22511.5623-0.39890.4550.0355-0.02750.5263-0.02490.401-11.7527-4.3623-15.5022
50.66660.43580.89880.9656-0.46426.5674-0.043-0.32580.12950.4512-0.0773-0.1985-1.08840.6962-0.03320.5013-0.07420.01750.5263-0.00250.3663-19.10365.65750.6244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 615 through 641 )A615 - 641
2X-RAY DIFFRACTION2chain 'A' and (resid 642 through 695 )A642 - 695
3X-RAY DIFFRACTION3chain 'A' and (resid 696 through 752 )A696 - 752
4X-RAY DIFFRACTION4chain 'A' and (resid 753 through 760 )A753 - 760
5X-RAY DIFFRACTION5chain 'A' and (resid 761 through 775 )A761 - 775

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