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- PDB-7qa7: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7qa7
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with Cyclopropanemethylamine
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
cyclopropylmethanamine / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 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)20,8812
Polymers20,8101
Non-polymers711
Water23413
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7624
Polymers41,6202
Non-polymers1422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)50.197, 69.361, 118.137
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-9L6 / cyclopropylmethanamine


Mass: 71.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9N / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 50.22 %
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: 0.9655 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: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.36→46.2 Å / Num. all: 17184 / Num. obs: 8764 / % possible obs: 90.3 % / Redundancy: 2 % / Biso Wilson estimate: 52.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Net I/σ(I): 12.4 / Num. measured all: 51552
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
2.36-2.44421.46317078630.4860.6511.606146.3
6.138-46.1994.20.02922635420.9990.0150.03335.297.5

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Processing

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

4zct


Resolution: 2.36→46.2 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 744 4.64 %
Rwork0.199 15284 -
obs0.2014 8760 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.81 Å2 / Biso mean: 60.6277 Å2 / Biso min: 35.72 Å2
Refinement stepCycle: final / Resolution: 2.36→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 5 13 1135
Biso mean--54.57 53.89 -
Num. residues----136
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 (%)
2.36-2.540.32681380.29213099323798
2.54-2.80.33071370.28973095323298
2.8-3.20.30381240.25263090321498
3.2-4.030.2431900.18873005319597
4.03-46.20.20811550.15562995315096
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)
13.91180.6803-0.15896.13470.48084.88820.06660.0222-0.197-0.056-0.12-0.1154-0.16030.4293-0.0230.34970.0034-0.050.39260.0080.4316-19.4608-11.1939-25.4713
23.25540.9306-0.27874.72941.0044.42820.0299-0.4927-0.11050.12120.066-0.5835-0.17310.60370.07020.40140.0058-0.04550.4155-0.00760.4377-16.1012-4.2706-23.4517
33.0655-0.6018-0.02452.98681.55123.196-0.2713-0.11-0.67170.2101-0.0166-0.16780.3217-0.30410.36370.24060.0057-0.00620.29820.03480.4315-21.1404-14.874-22.9518
44.34450.2995-1.15345.3057-0.22994.4164-0.4905-0.5043-0.00780.54430.15540.0522-0.3104-0.8510.00540.45240.0330.00590.4653-0.01210.4028-29.2217-9.9265-15.9794
53.77090.99-0.84693.2035-0.22433.1678-0.13280.1928-0.4564-0.43640.1359-0.20020.5193-0.19550.03870.416-0.016-0.02550.3573-0.04750.4074-23.4747-14.1516-25.4272
66.22611.5341-1.02187.8849-2.14462.7124-0.0714-0.153-0.88140.2031-0.0690.120.64430.03360.15140.52930.06850.05870.4644-0.01210.6043-18.0085-21.7262-31.2003
72.0447-1.9133-3.10356.83196.22948.1709-1.2965-2.2107-0.63230.39721.540.1313-1.2750.21180.05160.94010.14140.03720.88260.01210.8602-8.7064-20.5956-18.0156
84.8602-0.7735-0.04716.92252.46041.8588-0.158-0.0066-0.56220.43870.187-0.10070.0563-0.291-0.14330.53840.04590.01280.53740.06370.5839-8.1915-21.8399-27.5893
93.5477-3.2937-1.90355.36163.63972.6149-0.5854-1.25550.5231.24970.4317-0.41971.02760.6295-0.16460.82690.0117-0.04660.8259-0.01270.8355-11.7038-4.7249-15.6168
103.2481-0.56630.27341.8692-3.19635.5424-0.0987-0.57120.67180.8071-0.5851-0.4182-0.82310.79530.60320.6362-0.1075-0.0310.80030.03530.6795-18.93415.77580.6522
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 679 )A663 - 679
5X-RAY DIFFRACTION5chain 'A' and (resid 680 through 695 )A680 - 695
6X-RAY DIFFRACTION6chain 'A' and (resid 696 through 709 )A696 - 709
7X-RAY DIFFRACTION7chain 'A' and (resid 710 through 741 )A710 - 741
8X-RAY DIFFRACTION8chain 'A' and (resid 742 through 752 )A742 - 752
9X-RAY DIFFRACTION9chain 'A' and (resid 753 through 760 )A753 - 760
10X-RAY DIFFRACTION10chain 'A' and (resid 761 through 775 )A761 - 775

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