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- PDB-7qd3: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7qd3
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with morpholine
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 / nuclear envelope / 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
morpholine / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsDuclovel, C. / Gelin, M. / Krimm, I. / Cerdan, R. / Guichou, J.-F.
Funding support France, 1items
OrganizationGrant numberCountry
Montpellier University of Excellence (MUSE)MUSE_MALTA 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
DepositionNov 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 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)20,9843
Polymers20,8101
Non-polymers1742
Water30617
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9696
Polymers41,6202
Non-polymers3484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)50.698, 68.653, 117.924
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-6LR / morpholine


Mass: 87.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
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: 0.96456 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: 0.96456 Å / Relative weight: 1
ReflectionResolution: 2.43→58.96 Å / Num. all: 15584 / Num. obs: 7936 / % possible obs: 98.5 % / Redundancy: 2 % / Biso Wilson estimate: 59.37 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.056 / Rrim(I) all: 0.131 / Net I/σ(I): 9.8 / Num. measured all: 41491
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
2.43-2.5221.06715037670.5670.5141.1891.494.9
9.08-58.964.20.0477091700.9960.0270.05526.594.5

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Processing

Software
NameVersionClassification
PHENIXv1.19refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 2.43→58.96 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2788 390 4.91 %
Rwork0.2267 13822 -
obs0.2292 7933 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.52 Å2 / Biso mean: 66.4809 Å2 / Biso min: 41.76 Å2
Refinement stepCycle: final / Resolution: 2.43→58.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 12 17 1109
Biso mean--68.27 60.32 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.610.43791370.33942720285795
2.61-2.880.4111700.32692786295699
2.88-3.290.3351410.29312816295797
3.29-4.150.26371300.20422762289297
4.15-58.960.22121350.18582738287395
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)
19.6084-3.7404-6.24149.64698.17567.6519-0.11290.231-0.6686-0.1789-0.65710.5211-0.34780.0210.57310.52030.0082-0.09250.2862-0.00250.4741-19.6954-11.0991-25.4198
29.54531.8471-0.23118.33083.91921.92080.13180.158-0.3511-0.3237-0.008-0.7195-0.36910.2279-0.10690.4930.0202-0.02860.34780.07440.4089-16.7296-6.9454-27.9551
35.28180.2613-1.70119.0081-1.316.4908-0.3853-0.1972-0.59980.1660.12470.00580.82890.11060.28710.37940.001-0.04840.3706-0.00240.4183-25.5095-15.8384-20.4951
49.5552-6.8435-5.66886.58893.93143.2397-0.1535-1.13850.00570.91210.7325-0.649-0.00120.559-0.55750.59270.0016-0.0910.51750.04230.4708-10.6945-15.8662-24.4371
55.4895-0.63881.47795.0758-3.29385.6078-0.1841-0.43980.62630.7221-0.2686-0.607-0.82961.29080.32470.6066-0.0908-0.05330.73530.01110.6293-19.21645.70130.7583
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 653 )A631 - 653
3X-RAY DIFFRACTION3chain 'A' and (resid 654 through 702 )A654 - 702
4X-RAY DIFFRACTION4chain 'A' and (resid 703 through 760 )A703 - 760
5X-RAY DIFFRACTION5chain 'A' and (resid 761 through 775 )A761 - 775

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