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- PDB-7q3m: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7q3m
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 3-hydroxypiperidine
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
(3S)-piperidin-3-ol / Guanidinium / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
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)21,2947
Polymers20,8101
Non-polymers4846
Water63135
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,58814
Polymers41,6202
Non-polymers96712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)50.440, 67.423, 116.781
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 (E. coli)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-GZ6 / Guanidinium


Mass: 60.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH6N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-8O9 / (3S)-piperidin-3-ol / (S)-3-Hydroxypiperidine


Mass: 101.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
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: 1.88→33.71 Å / Num. all: 53738 / Num. obs: 11693 / % possible obs: 96.4 % / Redundancy: 2.481 % / Biso Wilson estimate: 44.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05955 / Rrim(I) all: 0.083 / Χ2: 0.817 / Net I/σ(I): 8.07 / Num. measured all: 75341
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.88-1.992.4310.72420.465021509611080.1672.53595.7
1.99-2.132.3821.0210.9510874476245660.3831.29395.9
2.13-2.32.5330.5561.7910883444442970.6280.69696.7
2.3-2.522.5640.3013.2910354410040380.8570.37698.5
2.52-2.812.510.175.539098373536240.960.21297
2.81-3.242.3930.07411.317360325830760.9910.09494.4
3.24-3.972.570.03622.446984277227170.9980.04598
3.97-5.592.460.02730.795020214020410.9980.03495.4
5.59-33.712.5620.02634.142911119311360.9990.03295.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 2.2→33.71 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 943 4.98 %
Rwork0.2018 17992 -
obs0.2034 10377 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119 Å2 / Biso mean: 55.9707 Å2 / Biso min: 30.71 Å2
Refinement stepCycle: final / Resolution: 2.2→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 59 35 1161
Biso mean--67.18 53.03 -
Num. residues----131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.320.3581370.27452602273998
2.32-2.460.26741370.23852599273699
2.46-2.650.31161280.252609273798
2.65-2.920.26281340.2292548268296
2.92-3.340.27551370.22672500263795
3.34-4.210.18751390.1762618275798
4.21-33.710.20851310.17852516264795
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)
15.494-0.98682.5344.4971-3.17962.8114-0.05970.20180.29530.0122-0.11860.0888-0.0464-0.02270.05540.3712-0.00220.06120.3404-0.02390.3518-5.6093-22.6047-25.0044
27.1122-1.3545.12586.8668-6.81738.8820.1175-0.76410.1560.28770.48470.6641-0.132-0.5904-0.3170.38220.02140.03250.3765-0.0070.4128-8.9252-29.6777-22.8572
33.7304-0.10910.71464.2896-0.39383.8779-0.1341-0.06690.38770.14920.0260.0102-0.27740.1780.08690.2577-0.00810.03670.3034-0.00790.344-1.5764-18.8256-23.4673
49.045-4.73930.71173.03180.92024.4064-0.2352-0.65650.19671.52330.193-0.13-0.03860.06410.18230.6123-0.0136-0.03080.4814-0.02230.454-15.995-13.279-25.0197
55.3799-5.51147.25196.1862-7.66479.882-0.9043-0.7537-0.50060.42391.256-0.112-0.7662-1.8585-0.28110.7994-0.1670.33150.7639-0.10790.8109-13.0361-29.7606-15.1052
65.03780.30272.57594.6339-2.85255.8489-0.1148-0.43350.22220.06810.32570.1090.2208-1.282-0.29640.5139-0.01070.09220.7068-0.12860.4441-5.2756-39.2118-1.0748
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 706 )A642 - 706
4X-RAY DIFFRACTION4chain 'A' and (resid 707 through 752 )A707 - 752
5X-RAY DIFFRACTION5chain 'A' and (resid 753 through 760 )A753 - 760
6X-RAY DIFFRACTION6chain 'A' and (resid 761 through 773 )A761 - 773

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