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

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Basic information

Entry
Database: PDB / ID: 7pvg
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with isonicotinic acid
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
pyridine-4-carboxylic acid / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDuclovel, C. / Gelin, M. / Krimm, I. / Cerdan, R. / Guichou, J.-F.
Funding support France, 2items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI) France
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 1.1Oct 26, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...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)20,9332
Polymers20,8101
Non-polymers1231
Water27015
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8664
Polymers41,6202
Non-polymers2462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2250 Å2
ΔGint-8 kcal/mol
Surface area14380 Å2
Unit cell
Length a, b, c (Å)50.126, 68.668, 117.654
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-S3V / pyridine-4-carboxylic acid


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
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: 2.27→59.31 Å / Num. obs: 9628 / % possible obs: 99.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 55.03 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.064 / Rrim(I) all: 0.129 / Net I/σ(I): 6.4 / Num. measured all: 37422
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
2.27-2.353.91.09933859340.4130.6281.273197.9
9.09-59.313.10.0745311740.9930.0450.08715.395.9

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIXv1.19refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 2.27→59.31 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 846 4.9 %
Rwork0.2248 16428 -
obs0.226 9625 95.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.21 Å2 / Biso mean: 67.7758 Å2 / Biso min: 44.49 Å2
Refinement stepCycle: final / Resolution: 2.27→59.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 9 15 1106
Biso mean--71.39 61.15 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.27-2.410.38591310.33762680281193
2.41-2.60.29621550.29992776293197
2.6-2.860.3361150.32232778289396
2.86-3.280.3051580.26152767292596
3.28-4.120.2751490.2152726287596
4.13-59.310.17631380.17582701283994
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)
19.6715-2.6708-6.42378.31526.46922.26240.35670.3048-0.1141-0.05-0.4138-0.3171-0.7749-0.43570.01760.49380.0954-0.12320.29990.04470.4292-19.527-11.2958-25.5708
29.60151.0390.96229.95382.60471.9011-0.00650.39950.3549-0.0988-0.1065-0.7429-0.41920.35190.11680.3918-0.0024-0.00640.32910.09530.3655-16.7314-7.1543-28.1814
36.7552-0.8663-2.07999.1763-0.65899.2186-0.2618-1.0052-0.64930.5590.21490.05810.6351-0.56840.09440.4533-0.0636-0.02070.46330.05240.3846-28.092-13.5176-14.5605
45.62590.2732-2.03835.87910.10966.6583-0.17690.1596-0.3785-0.2389-0.0005-0.13110.5081-0.10770.21410.3126-0.0297-0.04140.3041-0.03110.3256-23.6494-14.0765-25.4562
54.5950.4912-2.06875.0509-0.23016.1073-0.57090.695-1.6689-1.03990.0359-0.18881.48110.17280.57420.71240.050.11150.4084-0.06940.681-19.4238-23.2482-32.7738
62.796-6.45480.90576.37261.70023.9651-0.6152-0.7354-0.35662.1030.0821-0.06970.5180.39520.66740.79020.00620.00820.52860.14230.602-9.6144-19.7875-24.5751
79.4199-0.2515-6.64491.5799-1.61336.5841-1.3287-1.57161.77860.85781.03920.52991.06091.43360.1970.97830.0526-0.34861.0540.17081.2884-13.2947-3.8306-13.8138
88.4835-2.1121-0.7818.299-6.65796.1991-0.4941-0.94620.1561-0.0764-0.2987-1.2147-1.12212.45371.38660.8295-0.1630.00280.98850.17460.6336-19.21135.6525-0.7715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 615 through 630 )A615 - 630
2X-RAY DIFFRACTION2chain 'A' and (resid 631 through 653 )A631 - 653
3X-RAY DIFFRACTION3chain 'A' and (resid 654 through 679 )A654 - 679
4X-RAY DIFFRACTION4chain 'A' and (resid 680 through 695 )A680 - 695
5X-RAY DIFFRACTION5chain 'A' and (resid 696 through 706 )A696 - 706
6X-RAY DIFFRACTION6chain 'A' and (resid 707 through 753 )A707 - 753
7X-RAY DIFFRACTION7chain 'A' and (resid 754 through 761 )A754 - 761
8X-RAY DIFFRACTION8chain 'A' and (resid 762 through 773 )A762 - 773

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