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

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Basic information

Entry
Database: PDB / ID: 9hsm
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with N-hydroxy-2-methylpropanimidamide
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
: / BETA-MERCAPTOETHANOL / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 N-hydroxy-2-methylpropanimidamide
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

Downloads & links

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Assembly

Deposited unit
A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7603
Polymers20,5801
Non-polymers1802
Water77543
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5206
Polymers41,1602
Non-polymers3614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2520 Å2
ΔGint-9 kcal/mol
Surface area13660 Å2
Unit cell
Length a, b, c (Å)50.124, 67.522, 117.202
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: 20579.881 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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1IWW / 2-methyl-~{N}'-oxidanyl-propanimidamide


Mass: 102.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 48.95 %
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: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / 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: 1.96→46.09 Å / Num. obs: 22386 / % possible obs: 96.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 43.47 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.035 / Rrim(I) all: 0.074 / Χ2: 1 / Net I/σ(I): 11.4
Reflection shellResolution: 1.96→2.01 Å / % possible obs: 96.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 1.765 / Num. measured all: 4051 / Num. unique obs: 973 / CC1/2: 0.346 / Rpim(I) all: 0.959 / Rrim(I) all: 2.023 / Χ2: 0.87 / Net I/σ(I) obs: 0.7

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→46.09 Å / SU ML: 0.2286 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1074 4.8 %
Rwork0.2114 21312 -
obs0.2125 22386 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.79 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 11 43 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771072
X-RAY DIFFRACTIONf_angle_d0.77991451
X-RAY DIFFRACTIONf_chiral_restr0.0527169
X-RAY DIFFRACTIONf_plane_restr0.0048178
X-RAY DIFFRACTIONf_dihedral_angle_d13.3136385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.140.30331320.29622721X-RAY DIFFRACTION95.39
2.14-2.260.25841480.26812719X-RAY DIFFRACTION93.69
2.26-2.40.32971140.26822610X-RAY DIFFRACTION90.56
2.4-2.580.31781450.24642683X-RAY DIFFRACTION94.58
2.58-2.840.24221350.25712703X-RAY DIFFRACTION94.47
2.84-3.250.25611400.22472695X-RAY DIFFRACTION93.72
3.25-4.10.21351240.18872565X-RAY DIFFRACTION89.31
4.1-46.090.19951360.17962616X-RAY DIFFRACTION90.8
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)
15.326457083240.4824238125861.497638264535.05289530206-0.9737484510691.97392890713-0.0476712033857-0.2798810922270.2777890622370.408794735907-0.09723062556060.119438176883-0.1092406252220.04397497135130.141196233480.3476141364740.01010321509280.05200472285840.390727600516-0.03175254871750.314471864599-2.22682064807-22.2026187977-22.1049326695
22.68004640114-1.997902298871.186666867995.222229914261.543412656072.121734636440.0634762153114-0.4718571425410.5977381743770.379621896715-0.1826087445160.130922917143-0.308247376106-0.2211033004790.07429842008690.441324784424-0.0131849456655-0.03075331531330.446921326633-0.0186027907770.403974393171-11.5385640676-12.8309547347-27.3845783575
36.15134077202-3.3575163115.923388250432.67102291012-2.170825212347.03694675019-0.260231481364-1.30786319230.821985878840.1158272179560.234574998822-0.295671574770.6390447079-1.309835274030.02177665942510.79274046053-0.04286131266460.0776581380510.794043060797-0.1831941083770.550989436646-7.41589441609-36.1480851553-6.20164131228
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 695 )616 - 6951 - 80
22chain 'A' and (resid 696 through 753 )696 - 75381 - 112
33chain 'A' and (resid 754 through 772 )754 - 772113 - 131

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