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

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Basic information

Entry
Database: PDB / ID: 7pve
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 4-bromo-1H-imidazole
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
4-bromo-1H-imidazole / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_assembly ...pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1043
Polymers20,8101
Non-polymers2942
Water48627
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2086
Polymers41,6202
Non-polymers5884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2210 Å2
ΔGint-10 kcal/mol
Surface area15410 Å2
Unit cell
Length a, b, c (Å)50.497, 70.089, 118.448
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-ES3 / 4-bromo-1H-imidazole


Mass: 146.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H3BrN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8
Details: PEG 4000 19%, TRIS pH8 0.1M 6-7-8-9-10% Guanidine HCL 5-6-7% Glycerol

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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: 2.01→41.01 Å / Num. obs: 8630 / % possible obs: 84.6 % / Redundancy: 2 % / Biso Wilson estimate: 44.15 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.062 / Rrim(I) all: 0.1 / Net I/σ(I): 6.5 / Num. measured all: 47481 / Scaling rejects: 158
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.071.91.11828868440.1580.9891.4991.278
9.01-41.012.30.0465892550.9950.0350.05817.277.9

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Processing

Software
NameVersionClassification
PHENIXv1.19refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 2.39→40.97 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 746 4.94 %
Rwork0.1999 14354 -
obs0.2014 8540 93.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.1 Å2 / Biso mean: 51.1786 Å2 / Biso min: 29.44 Å2
Refinement stepCycle: final / Resolution: 2.39→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 18 27 1132
Biso mean--55.2 45.33 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.570.28541320.25473004313697
2.57-2.830.29921490.24452822297192
2.83-3.240.24481420.24832861300394
3.24-4.080.25571580.18712866302493
4.09-40.970.18211650.16772801296692
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)
16.01090.2945-1.94746.88661.5583.86150.0412-0.05590.08250.00010.0004-0.12260.09480.1785-0.11590.2683-0.0032-0.08340.2440.0210.2799-18.4208-8.4495-24.6865
26.40710.4503-1.47594.86540.04055.01970.0470.2426-0.27950.18580.30540.29720.2395-0.5515-0.36280.1850.0109-0.05020.1893-0.00680.3432-21.2868-14.712-23.3961
34.7299-0.001-2.12574.37920.73832.5491-0.1246-0.2746-0.26970.3278-0.04050.04520.34860.01520.18580.2952-0.0239-0.04310.28860.02690.2664-26.6116-12.0214-20.6115
46.55291.2670.01527.9698-3.01923.6965-0.0125-0.5795-0.42690.4796-0.2523-0.11260.25160.14360.25510.31040.04780.00520.3193-0.01820.3039-13.6987-21.7015-28.3858
57.8056-6.202-8.14588.35768.77492.00210.2877-1.6571-0.55020.82740.8085-0.09561.64621.674-1.08410.87910.0907-0.26170.761-0.01850.6906-11.9254-4.882-15.6544
67.0582-1.5915-0.66046.1709-7.50362.0023-0.1008-1.3122-0.06510.5303-1.0515-0.78250.35712.15591.09980.6449-0.07210.04690.97870.14820.5136-18.94595.84520.7219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 615 through 641 )A615 - 641
2X-RAY DIFFRACTION2chain 'A' and (resid 642 through 662 )A642 - 662
3X-RAY DIFFRACTION3chain 'A' and (resid 663 through 695 )A663 - 695
4X-RAY DIFFRACTION4chain 'A' and (resid 696 through 752 )A696 - 752
5X-RAY DIFFRACTION5chain 'A' and (resid 753 through 760 )A753 - 760
6X-RAY DIFFRACTION6chain 'A' and (resid 761 through 775 )A761 - 775

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