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

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Basic information

Entry
Database: PDB / ID: 4zcr
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with phosphocholine
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
PHOSPHOCHOLINE / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Oct 19, 2016Group: Data collection
Revision 1.2Feb 8, 2017Group: Data collection
Revision 1.3Aug 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 1.4Jan 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)20,9942
Polymers20,8101
Non-polymers1841
Water1,63991
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9894
Polymers41,6202
Non-polymers3682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area2950 Å2
ΔGint5 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.620, 69.570, 117.860
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-PC / PHOSPHOCHOLINE / Phosphocholine


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG 4k

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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: 1.8→46.51 Å / Num. obs: 18719 / % possible obs: 99.63 % / Redundancy: 6.4 % / Rsym value: 0.054 / Net I/σ(I): 14.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHASERphasing
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 1.8→46.51 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.966 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 927 4.7 %RANDOM
Rwork0.17641 ---
obs0.17892 18719 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: 47.198 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0 Å2
2--0.07 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 11 91 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021082
X-RAY DIFFRACTIONr_bond_other_d0.0030.021069
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9631467
X-RAY DIFFRACTIONr_angle_other_deg1.0763.0042461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70324.46847
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61215203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.918155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021160
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02233
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_it3.6024.435514
X-RAY DIFFRACTIONr_mcbond_other3.6064.428513
X-RAY DIFFRACTIONr_mcangle_it3.766.629640
X-RAY DIFFRACTIONr_mcangle_other3.7576.639641
X-RAY DIFFRACTIONr_scbond_it3.1784.861567
X-RAY DIFFRACTIONr_scbond_other3.1754.863568
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8597.132826
X-RAY DIFFRACTIONr_long_range_B_refined4.35436.5961254
X-RAY DIFFRACTIONr_long_range_B_other4.35236.6141255
X-RAY DIFFRACTIONr_rigid_bond_restr1.99232149
X-RAY DIFFRACTIONr_sphericity_free26.232533
X-RAY DIFFRACTIONr_sphericity_bonded9.45652190
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 68 -
Rwork0.29 1325 -
obs--98.45 %

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