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- PDB-7q2m: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7q2m
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with but-3-yn-2-amine 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 / nuclear envelope / 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
(2S)-but-3-yn-2-amine / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 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)20,9483
Polymers20,8101
Non-polymers1382
Water63135
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8976
Polymers41,6202
Non-polymers2764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2160 Å2
ΔGint-8 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.300, 68.991, 117.534
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-8PN / (2S)-but-3-yn-2-amine / 2-Aminobutin


Mass: 69.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7N / Feature type: SUBJECT OF INVESTIGATION
#3: 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: 2.45 Å3/Da / Density % sol: 49.8 %
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 PILATUS 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: 2.08→40.64 Å / Num. obs: 12612 / % possible obs: 99.43 % / Redundancy: 5.2 % / Biso Wilson estimate: 47.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04953 / Net I/σ(I): 17.18
Reflection shellResolution: 2.08→2.154 Å / Num. unique obs: 12612 / CC1/2: 0.999

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Processing

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

4zct


Resolution: 2.08→40.64 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 1155 4.97 %
Rwork0.2087 22101 -
obs0.2101 12604 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.01 Å2 / Biso mean: 59.4236 Å2 / Biso min: 36.97 Å2
Refinement stepCycle: final / Resolution: 2.08→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 17 35 1106
Biso mean--74.32 55.95 -
Num. residues----130
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.08-2.170.30671450.3001278499
2.17-2.290.36091470.2867277798
2.29-2.430.30651410.2462277398
2.43-2.620.27721470.2441275698
2.62-2.880.26871460.2395275498
2.88-3.30.25431390.2494279498
3.3-4.160.17011500.1922272198
4.16-40.640.23391400.1708274296
Refinement TLS params.Method: refined / Origin x: -19.7382 Å / Origin y: -12.0648 Å / Origin z: -21.6757 Å
111213212223313233
T0.3892 Å20.005 Å2-0.0292 Å2-0.4065 Å20.0588 Å2--0.4055 Å2
L1.9703 °2-0.0283 °2-0.2574 °2-2.6778 °2-0.2397 °2--1.8643 °2
S-0.0475 Å °-0.2591 Å °-0.2087 Å °0.2684 Å °-0.0254 Å °-0.303 Å °0.1276 Å °0.1724 Å °0.0618 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA615 - 772
2X-RAY DIFFRACTION1allX1
3X-RAY DIFFRACTION1allS1 - 47
4X-RAY DIFFRACTION1allB1

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