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

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Basic information

Entry
Database: PDB / ID: 7pui
TitleCrystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-pyridineboronic 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
pyridin-2-ylboronic acid / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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
DepositionSep 30, 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
Water37821
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 area2300 Å2
ΔGint-7 kcal/mol
Surface area15550 Å2
Unit cell
Length a, b, c (Å)50.401, 69.078, 117.835
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-86Z / pyridin-2-ylboronic acid / 2-Pyridineboronic acid / Pyridine-2-boronic acid


Mass: 122.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6BNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 50.09 %
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: 2.08→59.59 Å / Num. obs: 12538 / % possible obs: 98.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 47.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.046 / Rrim(I) all: 0.1 / Net I/σ(I): 8.7 / Num. measured all: 56095 / Scaling rejects: 8
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
2.08-2.144.21.322348911060.440.6951.5021.285.7
9.06-59.5940.0597301810.9960.0330.06821.398.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCT

4zct


Resolution: 2.08→59.59 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1115 4.88 %
Rwork0.2107 21713 -
obs0.2123 12533 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.76 Å2 / Biso mean: 59.5582 Å2 / Biso min: 37.04 Å2
Refinement stepCycle: final / Resolution: 2.08→59.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 0 9 21 1126
Biso mean--63.64 51.54 -
Num. residues----134
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 (%)
2.08-2.170.36881430.34242494263788
2.17-2.290.30971340.31772716285096
2.29-2.430.31771210.29342795291697
2.43-2.620.3388930.28922796288997
2.62-2.880.38951160.28742759287596
2.88-3.30.29451800.24982718289896
3.3-4.160.21581740.18192676285096
4.16-59.590.1761540.15252759291397
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)
16.6741-0.3939-0.9535.51760.58674.40670.10940.1444-0.108-0.0411-0.0259-0.16690.133-0.0768-0.00820.3393-0.0019-0.05140.29440.02180.4217-19.5912-11.2394-25.2947
26.97440.266-0.59545.62360.48582.75420.03780.30610.0611-0.12090.0765-0.5278-0.25840.1596-0.02770.30560.0075-0.01010.33160.04160.3647-16.7661-7.0213-27.9468
35.1724-0.7979-1.12354.15740.4512.3603-0.1547-0.4029-0.74040.40540.02080.20930.4397-0.12470.13940.3794-0.0123-0.03790.33440.05810.4001-24.8408-15.9125-21.7488
43.7484-4.72880.53726.2859-0.64450.0535-0.4274-0.6925-0.29081.30060.1485-0.25310.14620.26280.35670.57470.05760.00970.54420.10680.5863-9.0187-20.3732-24.9099
50.78790.493-1.45410.3495-0.41963.7939-0.167-0.8014-0.05840.54360.4327-0.06380.31131.167-0.21760.6905-0.0185-0.04670.95350.0790.6181-16.80042.577-4.405
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 706 )A654 - 706
4X-RAY DIFFRACTION4chain 'A' and (resid 707 through 752 )A707 - 752
5X-RAY DIFFRACTION5chain 'A' and (resid 753 through 775 )A753 - 775

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