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- PDB-7q3w: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7q3w
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with (R)-2-Aminobutanamide hydrochloride
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
(R)-2-Aminobutanamide / Guanidinium / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 28, 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)21,1775
Polymers20,8101
Non-polymers3664
Water2,396133
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,35310
Polymers41,6202
Non-polymers7338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)50.918, 69.002, 116.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-980-

HOH

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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-GZ6 / Guanidinium


Mass: 60.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH6N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-8R1 / (R)-2-Aminobutanamide / (2R)-2-azanylbutanamide


Mass: 102.135 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
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: 1.421→59.396 Å / Num. obs: 20816 / % possible obs: 92.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.11 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Rrim(I) all: 0.065 / Net I/σ(I): 14.5 / Num. measured all: 105773
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
1.421-1.59151.024598612030.5370.511.1481.478.9
4.67-59.3964.30.033516412020.9870.0190.03841.298.8

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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: 1.75→59.4 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 1860 4.84 %
Rwork0.1899 36560 -
obs0.1907 20794 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.7 Å2 / Biso mean: 35.2339 Å2 / Biso min: 18.27 Å2
Refinement stepCycle: final / Resolution: 1.75→59.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 30 133 1251
Biso mean--51.93 41.47 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.80.32631800.31912839301998
1.8-1.850.32451910.27932837302898
1.85-1.910.26471500.24242911306198
1.91-1.980.26691670.23552809297697
1.98-2.060.28391270.2342860298797
2.06-2.150.19111360.19622837297396
2.15-2.260.19211330.18582848298195
2.26-2.40.26181010.18072654275590
2.4-2.590.19611180.18732894301297
2.59-2.850.26571210.20112824294596
2.85-3.260.21971170.19512810292795
3.26-4.110.17111670.16792697286492
4.11-59.40.17671520.16672740289293
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)
12.3845-0.3091-0.56953.040.16513.2699-0.03440.1065-0.1646-0.1475-0.0254-0.08770.24580.0480.04350.17710.0065-0.01270.1531-0.01610.207-21.7294-12.7018-23.6609
29.0667-4.2123-2.1562.07490.63530.8722-0.451-0.9568-0.43550.94870.3961-0.560.33020.4289-0.00710.40450.08860.00780.48-0.00290.3609-8.5577-20.0293-24.9718
3-0.05460.1158-0.2973-0.16940.937.32770.07230.07910.0146-0.31980.1157-0.1637-0.29840.7013-0.310.2234-0.0389-0.00080.3598-0.00620.313-16.66582.215-4.7203
422.000122.00021.99982.00010.04811.0721-0.93622.498-0.0317-1.2448-1.9195-0.856-0.02310.8170.22650.33530.49050.32220.6009-27.3177-1.2917-13.2329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 615 through 706 )A615 - 706
2X-RAY DIFFRACTION2chain 'A' and (resid 707 through 752 )A707 - 752
3X-RAY DIFFRACTION3chain 'A' and (resid 753 through 775 )A753 - 775
4X-RAY DIFFRACTION4chain 'A' and (resid 801 through 801 )A801

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