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

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Basic information

Entry
Database: PDB / ID: 7pvf
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 3-hydroxy-1lambda6-thietane-1,1-dione
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
Guanidinium / 1,1-bis(oxidanylidene)thietan-3-ol / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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)21,1144
Polymers20,8101
Non-polymers3043
Water1448
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2298
Polymers41,6202
Non-polymers6096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2230 Å2
ΔGint-10 kcal/mol
Surface area15580 Å2
Unit cell
Length a, b, c (Å)50.680, 69.279, 118.081
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-HV2 / 1,1-bis(oxidanylidene)thietan-3-ol


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GZ6 / Guanidinium


Mass: 60.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH6N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 0
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: 2.31→59.82 Å / Num. obs: 9210 / % possible obs: 83.8 % / Redundancy: 1.6 % / Biso Wilson estimate: 54.53 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.058 / Rrim(I) all: 0.082 / Net I/σ(I): 5.1 / Num. measured all: 45976
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
2.31-2.391.50.59641838980.5040.5960.8430.980.5
8.96-59.821.80.0728524680.8720.0720.10112.477.2

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Processing

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

4zct


Resolution: 2.33→46.57 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 791 4.74 %
Rwork0.2081 15882 -
obs0.2107 9137 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.85 Å2 / Biso mean: 62.8668 Å2 / Biso min: 41.51 Å2
Refinement stepCycle: final / Resolution: 2.33→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 23 8 1113
Biso mean--66.64 63.89 -
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 (%)
2.33-2.480.31141320.28782671280398
2.48-2.670.30331340.24732697283198
2.67-2.940.27721060.29472692279898
2.94-3.360.29091110.25262644275597
3.36-4.240.24221800.19162597277797
4.24-46.570.2631280.16882581270995
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)
15.37430.0606-1.40675.11862.29876.36750.18630.1363-0.1156-0.0529-0.2917-0.0693-0.0171-0.35440.11470.44550.0265-0.03890.41420.00560.4592-20.1158-11.2898-24.4509
25.1308-1.002-1.23844.64863.20067.33030.0046-0.4321-0.14070.18880.1949-0.6668-0.31570.7364-0.18980.4097-0.0122-0.04610.37520.01860.4795-16.1368-4.3212-24.1858
34.702-1.24810.74323.36671.58172.8221-0.2284-0.3091-0.66220.3126-0.0221-0.08260.5681-0.06640.11920.35260.01420.00090.29590.01950.5024-21.8819-15.3399-22.8894
42.0427-6.57414.37352.1724-1.49696.8806-0.4275-0.835-0.60921.26360.2477-0.72181.06810.97930.28340.67260.0682-0.0670.83130.10350.5694-26.5914-13.0545-9.0922
55.2033-0.48730.23853.56340.51333.23360.05790.410.05310.0184-0.06970.2710.2418-0.5975-0.00890.4095-0.0277-0.02750.3649-0.00640.3817-28.1523-7.711-23.9795
63.58810.3163-2.4212.775-0.58853.771-0.06850.0606-0.57440.0141-0.13380.25910.64630.29640.18940.54120.05480.0050.4175-0.01570.5922-20.0932-21.982-27.7697
79.30162.12053.69116.51570.17315.9771-0.0989-0.9689-0.66151.60760.1276-0.24080.40230.0434-0.3160.5740.04880.030.52590.12520.5374-8.7286-21.0424-25.4904
81.7738-0.1359-0.93672.77062.41145.3091-0.7158-0.67690.7925-0.233-0.06560.7199-0.50420.89280.71110.9393-0.055-0.13020.83490.01840.9043-11.954-4.8305-15.5885
93.858-0.1707-0.75231.8761-2.57854.79240.161-1.01160.16191.336-0.7764-0.5998-0.8241.38870.58950.8567-0.26740.03290.99620.14790.5821-19.10115.77530.7646
102.00021.99981.99972.00041.99962.00012.5015-0.56042.2946-0.54160.69856.4332-6.8468-0.3733-3.29040.58550.62190.41890.7289-0.15340.7535-3.6239-17.9488-26.9913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 616 through 630 )A616 - 630
2X-RAY DIFFRACTION2chain 'A' and (resid 631 through 642 )A631 - 642
3X-RAY DIFFRACTION3chain 'A' and (resid 643 through 662 )A643 - 662
4X-RAY DIFFRACTION4chain 'A' and (resid 663 through 669 )A663 - 669
5X-RAY DIFFRACTION5chain 'A' and (resid 670 through 687 )A670 - 687
6X-RAY DIFFRACTION6chain 'A' and (resid 688 through 709 )A688 - 709
7X-RAY DIFFRACTION7chain 'A' and (resid 710 through 752 )A710 - 752
8X-RAY DIFFRACTION8chain 'A' and (resid 753 through 760 )A753 - 760
9X-RAY DIFFRACTION9chain 'A' and (resid 761 through 775 )A761 - 775
10X-RAY DIFFRACTION10chain 'A' and (resid 803 through 803 )A803

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