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- PDB-7q9v: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7q9v
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 1-(1,3-oxazol-4-yl)methanamine
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
1,3-oxazol-4-ylmethanamine / Guanidinium / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
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

Downloads & links

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Assembly

Deposited unit
A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2477
Polymers20,8101
Non-polymers4376
Water3,351186
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,49314
Polymers41,6202
Non-polymers87312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)50.699, 68.738, 116.881
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-1035-

HOH

21A-1058-

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.: 4 / Source method: obtained synthetically / Formula: CH6N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-9OI / 1,3-oxazol-4-ylmethanamine


Mass: 98.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 49.73 %
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: 0.96546 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: 1.31→40.8 Å / Num. obs: 32949 / % possible obs: 96.1 % / Redundancy: 2.15 % / Biso Wilson estimate: 20.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05205 / Rrim(I) all: 0.068 / Χ2: 0.832 / Net I/σ(I): 8.3 / Num. measured all: 196430
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
1.31-1.392.0881.4080.373087415409147850.1412.75296
1.39-1.482.0091.1550.642811614428139930.3311.51497
1.48-1.62.2320.5891.422922713461130950.6340.75897.3
1.6-1.762.220.3012.782649112369119310.870.38596.5
1.76-1.962.0780.1425.392209111194106300.9740.18295
1.96-2.272.1890.06212.621078986996270.9940.07897.5
2.27-2.772.2570.03721.4318147834880390.9970.04796.3
2.77-3.912.1190.02332.912422644658610.9980.0390.9
3.91-40.82.3590.01843.867984357433840.9990.02394.7

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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: 1.5→40.8 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 757 2.32 %
Rwork0.1814 59123 -
obs0.1819 32930 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.71 Å2 / Biso mean: 26.8471 Å2 / Biso min: 15.71 Å2
Refinement stepCycle: final / Resolution: 1.5→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 62 186 1343
Biso mean--37.94 33.74 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.550.32041400.30875975611597
1.55-1.620.31711480.27335983613197
1.62-1.690.33231420.26525935607797
1.69-1.780.21641400.23655944608496
1.78-1.890.25081450.20815843598895
1.89-2.040.19191430.19345955609896
2.04-2.240.18811440.17796002614697
2.24-2.560.18641380.17245988612697
2.56-3.230.17321330.18115745587893
3.23-40.80.20341290.14625753588293
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)
12.8014-0.3016-0.01223.40730.25840.2232-0.03070.0549-0.05-0.0235-0.0144-0.04360.04220.01210.05120.1390.0042-0.00520.1447-0.00860.0944-22.2628-11.4266-22.3013
29.5585-1.3518-1.66657.9659-0.81110.9593-0.064-0.5106-0.15170.4378-0.01150.09550.0670.01450.08020.19350.01690.02810.2294-0.02980.1-12.8762-21.4994-27.7858
30.3707-0.1589-1.45971.11552.73019.9302-0.0163-0.1404-0.0064-0.02330.2601-0.1286-0.18480.7178-0.30550.2037-0.0191-0.01030.27530.00930.1686-16.61942.3779-4.7675
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

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