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- PDB-4zcq: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 4zcq
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with choline
ComponentsCholinephosphate cytidylyltransferase
KeywordsTRANSFERASE / enzyme / malaria / cytidylyltransferase / phosphatidylcholine
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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CHOLINE ION / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsGuca, E. / Hoh, F. / Guichou, J.-F. / Cerdan, R.
Funding support France, 1items
OrganizationGrant numberCountry
EU Marie Curie ITN ParaMet290080 France
CitationJournal: Sci Rep / Year: 2018
Title: Structural determinants of the catalytic mechanism of Plasmodium CCT, a key enzyme of malaria lipid biosynthesis.
Authors: Guca, E. / Nagy, G.N. / Hajdu, F. / Marton, L. / Izrael, R. / Hoh, F. / Yang, Y. / Vial, H. / Vertessy, B.G. / Guichou, J.F. / Cerdan, R.
History
DepositionApr 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,9142
Polymers20,8101
Non-polymers1041
Water1,13563
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8294
Polymers41,6202
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_625-x+1,-y-3,z1
Buried area2810 Å2
ΔGint2 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.630, 69.350, 118.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Fragment: UNP residues 581-775
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: ctP, MAL13P1.86 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 24% PEG 3350, 0.08M NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972957 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972957 Å / Relative weight: 1
ReflectionResolution: 1.92→34.43 Å / Num. obs: 16280 / % possible obs: 99.22 % / Redundancy: 4 % / Rsym value: 0.038 / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 1.92→34.43 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 821 5.04 %random
Rwork0.2028 ---
obs0.204 16280 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 7 63 1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081070
X-RAY DIFFRACTIONf_angle_d0.9651454
X-RAY DIFFRACTIONf_dihedral_angle_d11.778382
X-RAY DIFFRACTIONf_chiral_restr0.04172
X-RAY DIFFRACTIONf_plane_restr0.004177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.04030.31481230.28852560X-RAY DIFFRACTION99
2.0403-2.19780.25751150.23672536X-RAY DIFFRACTION99
2.1978-2.41890.25511620.22582530X-RAY DIFFRACTION100
2.4189-2.76880.27721340.22852576X-RAY DIFFRACTION99
2.7688-3.48790.25421470.22642583X-RAY DIFFRACTION99
3.4879-34.43550.18931400.17582674X-RAY DIFFRACTION98

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