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

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Basic information

Entry
Database: PDB / ID: 9hsb
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with (5-methyl-3-isoxazolyl)methylamine
ComponentsCholinephosphate 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
: / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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 (5-methyl-3-isoxazolyl)methylamine
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: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0343
Polymers20,8101
Non-polymers2242
Water2,252125
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0696
Polymers41,6202
Non-polymers4494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2210 Å2
ΔGint-7 kcal/mol
Surface area15210 Å2
Unit cell
Length a, b, c (Å)50.441, 68.195, 117.016
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 Cholinephosphate cytidylyltransferase


Mass: 20810.123 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: ctP, MAL13P1.86 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-A1IWR / (5-methyl-1,2-oxazol-3-yl)methanamine


Mass: 112.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.547→58.51 Å / Num. obs: 33059 / % possible obs: 71.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.025 / Rrim(I) all: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 1.547→1.663 Å / % possible obs: 18.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.839 / Num. measured all: 4897 / Num. unique obs: 1076 / Rpim(I) all: 0.431 / Rrim(I) all: 0.947 / Net I/σ(I) obs: 1.7

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→58.51 Å / SU ML: 0.2644 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.5921
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 1614 4.88 %
Rwork0.1866 31445 -
obs0.188 33059 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.7 Å2
Refinement stepCycle: LAST / Resolution: 1.81→58.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 16 125 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621120
X-RAY DIFFRACTIONf_angle_d0.72051520
X-RAY DIFFRACTIONf_chiral_restr0.0553174
X-RAY DIFFRACTIONf_plane_restr0.0063190
X-RAY DIFFRACTIONf_dihedral_angle_d14.8288399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.4231580.35152717X-RAY DIFFRACTION97.66
1.86-1.920.36881360.29712653X-RAY DIFFRACTION94.32
1.92-1.990.27751440.26282728X-RAY DIFFRACTION96.02
1.99-2.070.22361500.2332668X-RAY DIFFRACTION94.66
2.07-2.160.27071280.21532697X-RAY DIFFRACTION95.7
2.17-2.280.25831110.20682643X-RAY DIFFRACTION92.39
2.28-2.420.26721350.21152641X-RAY DIFFRACTION93.22
2.42-2.610.20311180.1862700X-RAY DIFFRACTION95.95
2.61-2.870.19271120.20732122X-RAY DIFFRACTION74.79
2.87-3.290.24371250.18452689X-RAY DIFFRACTION94.78
3.29-4.140.16521650.1532537X-RAY DIFFRACTION91.47
4.14-58.510.18441320.15072650X-RAY DIFFRACTION93.04
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)
13.89689416591-1.2047315346-1.379077567876.076911013574.477125235083.74845019450.0897649904555-0.0475282525302-0.0194348628987-0.0320229740682-0.049114985761-0.242808913696-0.02807212287330.00644168825693-0.03599011088050.2061810593180.0336447992266-0.02748536056910.1951028349730.0472135793260.200050268008-18.379237882-8.19968969274-23.9012362111
23.55323038888-0.818161816535-1.27011143434.37743694532-0.04961970162712.48659551423-0.0935155684053-0.0577377252141-0.2923769872430.236476717143-0.03392245544050.03077988930960.343328255540.08001808512470.120853936470.22410782178-0.0165641075329-0.027398250410.190669344387-0.007805881210870.184774466229-23.9526840568-14.3723499612-22.7243704021
38.152409720980.05765170811131.244180924614.51029171829-0.6446678646.395728392930.0617993556927-0.7687997440350.02951153056760.612573047828-0.174647537494-0.394037970143-0.15549231467-0.0191876443815-0.007251708361880.4367586201730.0472971104409-0.05101232095080.311746415094-0.0216494604620.26985318167-14.1318075324-17.7745942923-27.5784155908
42.939493648221.18884948544-3.388539622352.475614293111.410039726379.387944895840.0385016313036-1.80216136534-0.5493698251451.86154333259-0.3259934765850.305163171640.1088052946090.1839394250190.2525087345820.5654210294960.03809032264260.01430372049480.4925547045530.01892842885160.358740343798-8.00589582595-24.3034527938-23.4857296395
56.56476822682-5.95948631334-6.740706331575.402785593766.113604116116.9004642283-0.284410214212-0.7102908062740.4474735101510.6027481236140.793597637172-0.5527211790310.5221023703961.14457655758-0.419051537870.3825622678580.055271481678-0.06199632075980.3901796838410.001585984325240.272314360813-10.4756677427-9.93770286186-20.8117148799
63.04244074591.496855661223.234281172473.418516170164.020540812697.60657510329-0.0969325252318-0.2318452892210.3213536947910.339076835009-0.206530059209-0.0689834278351-0.7424873137650.9168494374140.3605957623460.535496609681-0.111101929196-0.004076949680320.4471328283670.03493387223360.291556796876-19.10752243155.614662784720.560831225946
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 615 through 641 )615 - 6411 - 27
22chain 'A' and (resid 642 through 701 )642 - 70128 - 87
33chain 'A' and (resid 702 through 738 )702 - 73888 - 98
44chain 'A' and (resid 739 through 746 )739 - 74699 - 106
55chain 'A' and (resid 747 through 760 )747 - 760107 - 120
66chain 'A' and (resid 761 through 775 )761 - 775121 - 135

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