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

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Basic information

Entry
Database: PDB / ID: 7qad
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 1,4-Oxazepane hydrochloride
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 / nuclear envelope / 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
1,4-oxazepane / Guanidinium / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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
DepositionNov 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 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)21,0314
Polymers20,8101
Non-polymers2213
Water86548
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0638
Polymers41,6202
Non-polymers4436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)50.299, 68.740, 118.776
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-9OX / 1,4-oxazepane


Mass: 101.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GZ6 / Guanidinium


Mass: 60.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CH6N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8
Details: PEG 4000 19%, TRIS pH8 0.1M Guanidine HCl 6-7-8-9-10% Glycerol 5-6-7%

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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: 2.11→34.31 Å / Num. all: 23844 / Num. obs: 12157 / % possible obs: 92.1 % / Redundancy: 2 % / Biso Wilson estimate: 49.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Net I/σ(I): 16.5 / Num. measured all: 70562
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
2.11-2.18521.29238212020.4830.6611.454140.3
5.51-40.5924.40.02132517430.9990.0110.02450.498.3

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Processing

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

4zct


Resolution: 2.11→34.31 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1116 4.97 %
Rwork0.1995 21354 -
obs0.201 12155 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.12 Å2 / Biso mean: 62.673 Å2 / Biso min: 36.08 Å2
Refinement stepCycle: final / Resolution: 2.11→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 25 48 1140
Biso mean--90.91 59.21 -
Num. residues----130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.20.28631680.27392655282399
2.2-2.320.28911360.24212703283999
2.32-2.460.30271220.25262714283699
2.46-2.650.29221580.23272707286599
2.65-2.920.30771320.26232684281698
2.92-3.340.26331210.23142667278897
3.34-4.210.20921230.18572604272795
4.21-34.310.18861560.15822620277696
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)
15.37150.3997-0.05285.24920.3343.51510.1382-0.09780.2192-0.1186-0.13260.2302-0.1076-0.13020.00360.41720.01270.02450.3219-0.02110.3887-5.3488-23.0947-25.6515
26.20360.7171-0.28765.68870.21182.7091-0.0960.203-0.1837-0.1182-0.02110.42070.0908-0.34830.09410.39990.0070.0010.3679-0.04590.4067-8.3232-27.3375-28.1345
34.7350.6568-2.69175.54650.51657.6019-0.2341-1.40690.92510.96930.4722-0.9853-1.33410.9682-0.13250.70850.0246-0.13030.6338-0.20870.74410.8489-13.5287-11.9713
44.8769-0.06791.47714.79071.11473.9492-0.3251-0.77720.03610.66340.2831-0.12450.54840.1711-0.08760.49880.0186-0.00180.5035-0.0090.42294.1791-24.5376-16.0135
53.7823-0.4830.91292.70780.6211.9978-0.12820.11390.3171-0.13690.0208-0.0029-0.25270.00390.09990.4186-0.01450.03220.37690.0130.3931-1.4257-20.3145-25.5588
66.3031-1.18280.64186.02552.96792.3009-0.2469-0.26060.64120.3998-0.2051-0.1625-0.2929-0.06350.54730.58190.0699-0.06740.50170.0490.5261-8.4817-12.8841-29.1333
75.5533-1.07350.19998.0151.5763.4546-0.6726-0.26640.40720.5028-0.28980.79660.125-0.38930.72710.44190.03860.00850.5411-0.11450.6394-16.6971-12.5106-27.9173
81.3967-0.3340.675-0.0025-0.06740.3237-0.9267-2.5914-1.9727-0.0996-0.0194-0.4206-0.323-1.04790.60540.94080.12060.42381.20090.21431.1023-13.1038-30.1886-15.7287
92.579-0.56041.01921.79241.872.7235-0.2-1.0828-0.20770.6029-0.07570.62390.7708-1.75240.50590.7601-0.13170.11611.0355-0.06410.5687-5.5865-39.6644-1.2978
102.00061.99972.000622.00011.99984.792-3.223-0.3134-0.4791-0.7718-7.109-2.11573.9506-4.07760.34640.1864-0.15731.5516-0.22291.39333.3404-17.4802-32.7359
112.00012.00031.99962.00041.99892.00060.05062.95861.3669-0.9320.93251.782-9.45691.8248-1.01161.0370.0878-0.05411.04510.09461.1983-8.2684-11.8104-38.0706
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 662 )A654 - 662
4X-RAY DIFFRACTION4chain 'A' and (resid 663 through 679 )A663 - 679
5X-RAY DIFFRACTION5chain 'A' and (resid 680 through 695 )A680 - 695
6X-RAY DIFFRACTION6chain 'A' and (resid 696 through 741 )A696 - 741
7X-RAY DIFFRACTION7chain 'A' and (resid 742 through 752 )A742 - 752
8X-RAY DIFFRACTION8chain 'A' and (resid 753 through 760 )A753 - 760
9X-RAY DIFFRACTION9chain 'A' and (resid 761 through 773 )A761 - 773
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 1 )B1
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 2 )B2

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