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- PDB-7q9w: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7q9w
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 4-(aminomethyl)pyridin-2-amine
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
4-(aminomethyl)pyridin-2-amine / Guanidinium / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 15, 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)20,9933
Polymers20,8101
Non-polymers1832
Water2,432135
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9876
Polymers41,6202
Non-polymers3664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)50.593, 68.715, 117.119
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-9NN / 4-(aminomethyl)pyridin-2-amine


Mass: 123.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GZ6 / Guanidinium


Mass: 60.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH6N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
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: 1.803→59.27 Å / Num. all: 37419 / Num. obs: 19136 / % possible obs: 92.7 % / Redundancy: 2 % / Biso Wilson estimate: 31.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.021 / Rrim(I) all: 0.048 / Net I/σ(I): 17 / Num. measured all: 110445
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
1.803-1.86721.116371318810.5110.5471.2471.346.4
4.768-59.2674.80.024540411280.9990.0120.0274998.6

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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: 1.8→59.27 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 1686 4.76 %
Rwork0.1752 33712 -
obs0.1768 19129 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.28 Å2 / Biso mean: 35.8949 Å2 / Biso min: 20.52 Å2
Refinement stepCycle: final / Resolution: 1.8→59.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 18 135 1248
Biso mean--46.7 41.88 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.30681630.26662849301298
1.86-1.920.28571370.22942816295398
1.92-1.980.23011450.20722826297198
1.98-2.060.29241250.20272839296498
2.06-2.160.22421250.17222829295498
2.16-2.270.19441750.17562766294197
2.27-2.410.23321260.17822838296497
2.41-2.60.23841480.17852810295898
2.6-2.860.22021280.18292795292397
2.86-3.280.20251480.1882790293896
3.28-4.130.1751210.1582735285695
4.13-59.270.19431450.15942819296497
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)
10.7001-0.449-0.06410.66220.18540.117-0.01330.0023-0.0380.0457-0.0109-0.01350.0478-0.00500.18440.00020.00350.17890.00260.1856-22.3445-11.3967-22.4165
20.15130.0002-0.04890.1811-0.1554-0.0031-0.0366-0.1179-0.07120.086-0.09030.06230.0319-0.0247-00.24520.02680.00370.2468-0.02020.2588-13.1427-21.4625-27.8406
30.0808-0.06950.040.0463-0.08690.0482-0.0095-0.1397-0.0930.13760.0897-0.0061-0.12670.469-00.3732-0.0323-0.01710.42520.00790.2725-16.85072.5298-4.3079
42.00031.99992.00012.00012.00012-0.097-0.0387-2.7814-0.74160.2245-0.7058-0.01491.1551-0.13860.46170.11190.13170.34530.02740.8648-19.0061-19.1631-17.5268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 615 through 695 )A615 - 695
2X-RAY DIFFRACTION2chain 'A' and (resid 696 through 752 )A696 - 752
3X-RAY DIFFRACTION3chain 'A' and (resid 753 through 775 )A753 - 775
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 1 )C1

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