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

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Basic information

Entry
Database: PDB / ID: 9hsp
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with oxazol-4-yl-methylamine
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
1,3-oxazol-4-ylmethanamine / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 oxazol-4-yl-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: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8433
Polymers20,6471
Non-polymers1962
Water84747
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6866
Polymers41,2942
Non-polymers3924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2000 Å2
ΔGint-6 kcal/mol
Surface area14260 Å2
Unit cell
Length a, b, c (Å)50.370, 69.328, 118.385
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-9OI / 1,3-oxazol-4-ylmethanamine


Mass: 98.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.088→59.825 Å / Num. obs: 23632 / % possible obs: 88 % / Redundancy: 6.8 % / Biso Wilson estimate: 45.52 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.052 / Rrim(I) all: 0.137 / Net I/σ(I): 7.4
Reflection shellResolution: 2.088→2.21 Å / % possible obs: 28.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.342 / Num. measured all: 3831 / Num. unique obs: 558 / Rpim(I) all: 0.546 / Rrim(I) all: 1.451 / Net I/σ(I) obs: 1.3

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→59.82 Å / SU ML: 0.2966 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5782
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 1133 4.79 %
Rwork0.2045 22499 -
obs0.2061 23632 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.07 Å2
Refinement stepCycle: LAST / Resolution: 2.09→59.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 14 47 1117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861091
X-RAY DIFFRACTIONf_angle_d0.88491476
X-RAY DIFFRACTIONf_chiral_restr0.0543170
X-RAY DIFFRACTIONf_plane_restr0.0054182
X-RAY DIFFRACTIONf_dihedral_angle_d22.734143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.190.36181490.31712774X-RAY DIFFRACTION100
2.19-2.30.30551390.2752833X-RAY DIFFRACTION100
2.3-2.450.29641230.28932847X-RAY DIFFRACTION99.93
2.45-2.640.28251300.25772803X-RAY DIFFRACTION99.97
2.64-2.90.29231360.24752829X-RAY DIFFRACTION99.97
2.9-3.320.25581770.22432789X-RAY DIFFRACTION99.93
3.32-4.180.21371360.17642794X-RAY DIFFRACTION99.49
4.18-59.820.19411430.16352830X-RAY DIFFRACTION99.97
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)
15.15982071516-0.1080413777860.2012697239967.58265253395-1.388068992574.366353845360.0575146626001-0.1711228991760.02631963052440.227470615061-0.09460430319150.124160656045-0.101347416844-0.111650755034-0.01704677593850.326224289810.01038308288970.06653488141820.354233669373-0.02974648150830.367777137615-6.74527426456-26.3338304203-24.1072679803
25.99205810682-0.3687560887220.03287083438115.30201354825-1.723054910992.68107500620.04783890621480.90830543159-0.165009469437-0.8548512911490.06335945150680.5075467640730.08121259951380.0180598173874-0.01206564331880.411980491337-0.005928565525410.003158873282510.3606190477-0.03231237480070.364470722159-7.76680262749-24.75797246-32.6690109304
37.43703786147-0.100637641821.287147502839.13950180427-1.364467737465.2764926934-0.451239414377-0.9923864426260.6550913883570.9579835197980.314717184845-0.268780227775-0.5341962678120.3613533577390.1957946161560.3720714809130.00107498861183-0.04828758494120.449099877072-0.07200023634050.3346657623663.01831483194-21.010315127-14.6721687672
45.14121456285-0.05910299375610.741573390025.27452428363-1.256518898323.02314627372-0.05886704475950.04688116015130.229644645608-0.240134124623-0.009817679427280.153112375452-0.2745323509820.0540528895220.1605928532470.349116365252-0.0004283758927930.03046243664210.3896750343080.02310676014180.356916747219-1.45688960446-20.5322103569-25.4620577022
55.25280575010.5863948508264.28076882574.926758226254.014754917776.0843391212-0.2179666643070.01458696310071.013039427070.03192314525360.01958069215920.160087596501-0.407110379617-0.0266098326586-0.05924395936110.5441555424390.0419361256125-0.0194984244320.4090025694150.0306898201750.506190760537-6.74080519115-12.7506533856-31.1124278133
64.370554340730.449487303848-3.320872752165.780621140233.621683605988.307665308660.0557157529854-0.8815575151650.6377680135071.9602217522-0.0774500053404-0.144221717357-0.7231130356350.1956455860050.3554294249710.579668028403-0.00583141672447-0.00493383839170.527898540563-0.08583236411230.583361084396-16.3107180495-12.9378662033-25.3169342426
78.82152797787-2.90795590613.374576643215.31364049925-5.175999896265.08551162355-0.329851898923-2.19156152056-0.5009918700280.03472990898320.305807434402-0.8807558049030.635759836577-1.553105997960.3509437873231.14493006613-0.07740020143590.3329527173470.943955539032-0.03259772821450.845342973675-13.2192868697-30.0526501424-16.0793987295
88.51932112272-0.1035390303672.166992339813.9107774809-0.0871761896287.50024571748-0.480979843407-0.790561446472-0.224751160145-0.07004723319520.4689755067430.1568704232591.88399355384-2.226998444380.6403492209330.836637765042-0.1146311464860.1007638581020.791648528424-0.1787905455240.632515145677-5.31144068226-39.9914981247-1.63265125577
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 641 )616 - 6411 - 26
22chain 'A' and (resid 642 through 653 )642 - 65327 - 38
33chain 'A' and (resid 654 through 679 )654 - 67939 - 64
44chain 'A' and (resid 680 through 695 )680 - 69565 - 80
55chain 'A' and (resid 696 through 709 )696 - 70981 - 94
66chain 'A' and (resid 710 through 752 )710 - 75295 - 109
77chain 'A' and (resid 753 through 760 )753 - 760110 - 117
88chain 'A' and (resid 761 through 773 )761 - 773118 - 130

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