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

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Basic information

Entry
Database: PDB / ID: 4zcs
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with CDP-choline
ComponentsCholine-phosphate 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
Chem-CDC / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Choline-phosphate cytidylyltransferase
C: Choline-phosphate cytidylyltransferase
E: Choline-phosphate cytidylyltransferase
B: Choline-phosphate cytidylyltransferase
D: Choline-phosphate cytidylyltransferase
F: Choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,44314
Polymers124,8616
Non-polymers3,5838
Water6,143341
1
A: Choline-phosphate cytidylyltransferase
B: Choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9235
Polymers41,6202
Non-polymers1,3033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-19 kcal/mol
Surface area14440 Å2
MethodPISA
2
C: Choline-phosphate cytidylyltransferase
D: Choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9235
Polymers41,6202
Non-polymers1,3033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-23 kcal/mol
Surface area14010 Å2
MethodPISA
3
E: Choline-phosphate cytidylyltransferase
F: Choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5974
Polymers41,6202
Non-polymers9772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-22 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.631, 149.132, 175.598
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
Choline-phosphate cytidylyltransferase /


Mass: 20810.123 Da / Num. of mol.: 6 / Fragment: UNP residues 581-775
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1316600 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical
ChemComp-CDC / [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM / Citicoline


Mass: 488.324 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H26N4O11P2
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.2M NaF, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979338 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.45→113.67 Å / Num. obs: 52521 / % possible obs: 99.63 % / Redundancy: 9.35 % / Rsym value: 0.32 / Net I/σ(I): 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HL4

3hl4


Resolution: 2.45→113.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.35 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23413 2808 5.1 %RANDOM
Rwork0.18059 ---
obs0.18325 52521 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20 Å2
2---0.09 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.45→113.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6806 0 224 341 7371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.027185
X-RAY DIFFRACTIONr_bond_other_d0.0040.026895
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9849763
X-RAY DIFFRACTIONr_angle_other_deg1.1343.01115873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0225835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45424.763317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.972151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0931529
X-RAY DIFFRACTIONr_chiral_restr0.110.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027709
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021560
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0654.2483352
X-RAY DIFFRACTIONr_mcbond_other4.0654.2483351
X-RAY DIFFRACTIONr_mcangle_it6.1276.3534180
X-RAY DIFFRACTIONr_mcangle_other6.1276.3544181
X-RAY DIFFRACTIONr_scbond_it4.3644.6033833
X-RAY DIFFRACTIONr_scbond_other4.3634.6033833
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6976.7055583
X-RAY DIFFRACTIONr_long_range_B_refined9.19248.3967955
X-RAY DIFFRACTIONr_long_range_B_other9.19248.4027956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 200 -
Rwork0.28 3847 -
obs--99.7 %

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