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

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Basic information

Entry
Database: PDB / ID: 7pyb
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-Hydroxypyridine
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~{H}-pyridin-2-one / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsDuclovel, C. / Gelin, M. / Krimm, I. / Cerdan, R. / Guichou, J.-F.
Funding support France, 1items
OrganizationGrant numberCountry
Montpellier University of Excellence (MUSE)MUSE_MALTA 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 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9653
Polymers20,8101
Non-polymers1552
Water61334
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9316
Polymers41,6202
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2280 Å2
ΔGint-10 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.279, 69.229, 117.781
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-GZ6 / Guanidinium


Mass: 60.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH6N3
#3: Chemical ChemComp-HRZ / 1~{H}-pyridin-2-one


Mass: 95.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
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: 1.89→40.68 Å / Num. obs: 30264 / % possible obs: 94.5 % / Redundancy: 2.378 % / Biso Wilson estimate: 51.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04627 / Rrim(I) all: 0.059 / Χ2: 0.912 / Net I/σ(I): 9.32 / Num. measured all: 71979
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.89-22.4231.1280.4911041516045570.3122.2788.3
2-2.142.4121.0150.9611126489346130.4131.28194.3
2.14-2.312.2910.5741.839974452443530.7010.73396.2
2.31-2.532.3830.2673.439577414040190.8890.33997.1
2.53-2.832.4640.1346.959061377636770.9760.16997.4
2.83-3.262.350.0614.147496330331900.9950.07796.6
3.26-3.992.2930.032266066280526450.9980.0494.3
3.99-5.622.3990.02434.784966219920700.9980.03194.1
5.62-40.682.3440.02137.012672121211400.9990.02694.1

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Processing

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

4zct


Resolution: 2.03→40.68 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 34.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1225 4.98 %
Rwork0.2079 23373 -
obs0.2096 24598 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.02 Å2 / Biso mean: 62.4773 Å2 / Biso min: 36.99 Å2
Refinement stepCycle: final / Resolution: 2.03→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 0 16 34 1146
Biso mean--71.57 58.44 -
Num. residues----134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.110.43771270.39262536266394
2.11-2.210.35011410.33212656279797
2.21-2.320.40711360.40662542267895
2.32-2.470.31041410.28082615275697
2.47-2.660.2761400.24332679281998
2.66-2.930.24571380.26242624276297
2.93-3.350.25741360.23022593272996
3.35-4.220.22221320.17922587271995
4.22-40.680.20011340.15372541267594
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)
10.94970.17180.54621.3472-0.32680.27320.0602-0.1248-0.0519-0.0342-0.0322-0.13410.18170.245800.43590.00680.01910.42930.00390.4226-18.0855-8.2666-24.9336
21.1085-1.3580.62441.46250.48850.55080.03130.0859-0.12090.13880.17480.13480.0955-0.194-00.3628-0.03290.01660.35230.03330.3779-21.7251-15.3327-22.8086
32.1968-0.1111-0.33471.57760.01180.6175-0.0228-0.0743-0.0302-0.12720.05620.11210.0992-0.106800.3682-0.01670.00220.37720.01910.3799-26.5806-11.9903-20.5508
41.4024-0.37550.00850.4834-0.57450.1678-0.1565-0.3163-0.1995-0.0875-0.05850.0294-0.00060.007-00.49410.04790.03090.47740.02290.4803-13.4211-21.475-27.9344
50.13230.3834-0.42030.8871-1.22320.35040.1234-0.2997-0.25880.2148-0.2434-0.0197-0.20310.4381-00.6863-0.0943-0.03330.77130.01370.5965-16.7762.3843-4.4514
62.00032.001222.00021.99892.00070.4325-1.9115-2.70660.1830.16765.09935.5497-0.9104-0.6920.5998-0.0306-0.16110.91350.06730.9063-3.1611-17.5561-26.5373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 615 through 642 )A615 - 642
2X-RAY DIFFRACTION2chain 'A' and (resid 643 through 662 )A643 - 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 775 )A753 - 775
6X-RAY DIFFRACTION6chain 'A' and (resid 801 through 801 )A801

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