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- PDB-9hso: Crystal structure of C-terminal catalytic domain of Plasmodium fa... -

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Basic information

Entry
Database: PDB / ID: 9hso
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with pyridine
Componentscholine-phosphate cytidylyltransferase
KeywordsTRANSFERASE / CCT
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 / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAudebert, S. / Gelin, M. / Guichou, J.-F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE44-0012 France
CitationJournal: To Be Published
Title: Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with pyridine
Authors: Audebert, S. / Gelin, M. / Guichou, J.-F.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8053
Polymers20,6471
Non-polymers1582
Water45025
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6106
Polymers41,2942
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2020 Å2
ΔGint-8 kcal/mol
Surface area13050 Å2
Unit cell
Length a, b, c (Å)50.039, 69.599, 117.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein choline-phosphate cytidylyltransferase


Mass: 20646.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Deletion of a lysine rich loop (720 - 737)
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1316600 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-0PY / pyridine / Azabenzene / Azine


Mass: 79.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 50.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350 11.5%, NaF 210 mM, Glycerol 5.8%, MnCl2 15mM, 1,3 propandiol 3%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.25→59.84 Å / Num. obs: 15763 / % possible obs: 96.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 52.83 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Χ2: 0.97 / Net I/σ(I): 13.7
Reflection shellResolution: 2.25→2.32 Å / % possible obs: 96.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 1.203 / Num. measured all: 2882 / Num. unique obs: 875 / CC1/2: 0.397 / Rpim(I) all: 0.728 / Rrim(I) all: 1.421 / Χ2: 0.93 / Net I/σ(I) obs: 1

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→59.84 Å / SU ML: 0.2966 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.4048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 753 4.78 %
Rwork0.2179 15010 -
obs0.2201 15763 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.54 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 12 25 1049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691044
X-RAY DIFFRACTIONf_angle_d0.7661416
X-RAY DIFFRACTIONf_chiral_restr0.053168
X-RAY DIFFRACTIONf_plane_restr0.0062175
X-RAY DIFFRACTIONf_dihedral_angle_d15.1395362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.32711590.30043087X-RAY DIFFRACTION92.32
2.48-2.730.30021530.28493006X-RAY DIFFRACTION90.18
2.73-3.120.31941680.27042991X-RAY DIFFRACTION89.77
3.12-3.930.26661460.22992933X-RAY DIFFRACTION87.47
3.93-59.840.22841270.17272993X-RAY DIFFRACTION88.44
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)
14.3749838974-0.6247655789011.15037565392.11721747728-0.9315520290514.50278088732-0.0837192370423-0.2485953465290.3559959903240.106408391944-0.01429297508960.0652342391135-0.303130173107-0.08461383404810.08285288524590.410520568455-0.008579251262740.03439336834450.272049338355-0.04580299390020.379833136082-2.46151591475-22.0720382507-23.2722688285
28.40361367342-5.212396526782.074735654685.9684587014-0.8205852669053.27395186614-0.391447730286-1.304293193920.6575685317841.331340253420.3925264548550.08271988595990.215754650209-0.396221468711-0.08445248282850.615073900690.0430619078514-0.04391456837530.466926425081-0.09453836363360.549382300821-13.6717536606-13.9876906215-25.349149914
34.34614675866-5.56304612785.182011979819.40895560926-7.29287420656.26536108238-0.241067450248-1.06704221218-0.08486729946460.3789410335550.534753788391-0.141447234560.359851260596-1.63041352966-0.3450115546620.697985527576-0.169957488980.00359728953760.699635037619-0.05259873413310.504141500304-10.4764391891-30.4675514509-13.5628714423
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 616 through 702 )616 - 7021 - 87
22chain 'A' and (resid 703 through 746 )703 - 74688 - 104
33chain 'A' and (resid 747 through 771 )747 - 771105 - 129

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