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

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Basic information

Entry
Database: PDB / ID: 7qvn
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with(1H-pyrazol-5-yl)methanol
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
Guanidinium / 1~{H}-pyrazol-5-ylmethanol / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
DepositionJan 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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)21,0284
Polymers20,8101
Non-polymers2183
Water91951
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0578
Polymers41,6202
Non-polymers4376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)50.495, 68.918, 117.345
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-IRU / 1~{H}-pyrazol-5-ylmethanol


Mass: 98.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GZ6 / Guanidinium


Mass: 60.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH6N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 49.86 %
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: 2.21→34.02 Å / Num. obs: 10527 / % possible obs: 99.18 % / Redundancy: 1.9 % / Biso Wilson estimate: 47.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0275 / Net I/σ(I): 14.17
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 % / Resolution: 2.21→2.289 Å

Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.207105210.4410.6810.038999.18
0.0392580.9960.0210.04497.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 2.21→34.02 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 971 5.08 %
Rwork0.1887 18156 -
obs0.1902 10521 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.69 Å2 / Biso mean: 57.2209 Å2 / Biso min: 33.74 Å2
Refinement stepCycle: final / Resolution: 2.21→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 31 51 1170
Biso mean--83.29 54.72 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.21-2.330.31661310.2821260898
2.33-2.470.21511540.1877261897
2.47-2.660.31061380.2416262097
2.66-2.930.2341470.231255797
2.93-3.350.25981320.2098256895
3.36-4.220.20211390.163261197
4.23-34.020.17131300.158257495
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)
14.8594-0.5676-0.92065.10060.03244.7244-0.1443-0.1166-0.22730.08950.042-0.02550.3082-0.02740.09360.2335-0.0102-0.03070.2545-0.00030.2744-22.3552-11.504-22.3653
28.6244-2.2562-1.14867.1347-3.31432.11380.1007-0.4662-0.64290.0811-0.36510.04290.25050.10450.33490.49350.04410.050.4158-0.01170.3995-13.0626-21.3888-28.1454
31.832-0.0596-3.35892.225-0.74512.0919-0.1191-0.5659-0.28390.47670.226-0.2012-0.12061.59330.0310.52820.01-0.04890.78520.00820.4865-16.79662.4365-4.4581
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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