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

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Basic information

Entry
Database: PDB / ID: 9hse
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 5-(aminomethyl)pyridin-2-amine
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: 1.96 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-(aminomethyl)pyridin-2-amine
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)20,9332
Polymers20,8101
Non-polymers1231
Water66737
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8674
Polymers41,6202
Non-polymers2462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1820 Å2
ΔGint-0 kcal/mol
Surface area15000 Å2
Unit cell
Length a, b, c (Å)50.395, 69.420, 118.819
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-A1IWU / 5-(aminomethyl)pyridin-2-amine


Mass: 123.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 50.74 %
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: 0.965459 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.95→59.94 Å / Num. obs: 27573 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 42.28 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.052 / Rrim(I) all: 0.113 / Χ2: 0.89 / Net I/σ(I): 7.6
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 3.9 % / Num. unique obs: 1026 / CC1/2: 0.608 / Χ2: 0.63

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→59.94 Å / SU ML: 0.325 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.2639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 1425 5.17 %
Rwork0.2423 26148 -
obs0.2441 27573 95.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.64 Å2
Refinement stepCycle: LAST / Resolution: 1.96→59.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 9 37 1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651070
X-RAY DIFFRACTIONf_angle_d0.76981453
X-RAY DIFFRACTIONf_chiral_restr0.0552169
X-RAY DIFFRACTIONf_plane_restr0.0056181
X-RAY DIFFRACTIONf_dihedral_angle_d15.1437374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.030.41711660.37262612X-RAY DIFFRACTION95.4
2.03-2.110.32491560.31842601X-RAY DIFFRACTION95.4
2.11-2.210.3321660.28022656X-RAY DIFFRACTION97.44
2.21-2.320.30931150.30952631X-RAY DIFFRACTION95.31
2.32-2.470.36021320.30092643X-RAY DIFFRACTION96.15
2.47-2.660.37391220.28892695X-RAY DIFFRACTION96.87
2.66-2.930.32041210.30582609X-RAY DIFFRACTION93.91
2.93-3.350.29551470.27222563X-RAY DIFFRACTION94.39
3.35-4.220.24181460.20682534X-RAY DIFFRACTION92.77
4.22-59.940.23161540.19512604X-RAY DIFFRACTION94.87
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)
17.5724079831-1.015882319930.9722111378436.64896205848-1.623755822275.29662193769-0.0158434886882-0.1099420823230.2303031345510.17429598297-0.001917666074410.238246225990.0604089984847-0.01896145194410.00758818419480.1977082056590.03351920485730.01468965633130.255878276798-0.01634831332020.293174493893-6.98016552439-26.0282058867-25.9544125827
22.04091851904-0.619494640113-2.298504733695.971722718252.061773445812.93879716555-1.25951323408-2.075477536441.694822593581.769394785280.706913461967-1.60986809423-1.169555480950.160978439345-0.04626419550460.7768891525360.173973386532-0.3310788989240.732631436479-0.3547980076180.7472113881390.853974781504-16.8657099436-11.1373080627
35.12716300469-2.6034361035-0.1035844164677.5094831541-0.1609884097223.42107252386-0.05477222180240.1173798664810.721988430370.0798496195951-0.137459906263-0.776192836573-0.2874296058280.3354797577530.1941193357010.247848420479-0.0455646529969-0.01567900048990.306993193990.009559366760950.3972885353730.115552361758-20.1594572863-24.8884944728
45.24591396086-2.03886620371-4.984560401372.69806504513.86250589958.543872652580.168374102252-0.2460890634750.7958232640450.257040799408-0.4186549225390.06619477526450.150653003941-0.3254060420980.2208987148030.3577835540390.0362373632372-0.02772472191510.408699331066-0.006093339942460.504778524631-14.1188662991-14.1877560416-27.7679623393
51.3178431844-0.1330648664651.315129365082.249496247090.83837636682.53846850689-0.224532850519-1.349668428250.4832713585590.2657637110270.7306196633360.410382299508-0.21814541094-1.62350930822-0.7551942607180.493525550937-0.06002342278830.06636863579561.12897093594-0.02092799167730.640035643804-8.74138049583-36.6242759172-5.27435985637
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 617 through 653 )617 - 6533 - 39
22chain 'A' and (resid 654 through 669 )654 - 66940 - 55
33chain 'A' and (resid 670 through 701 )670 - 70156 - 87
44chain 'A' and (resid 702 through 752 )702 - 75288 - 111
55chain 'A' and (resid 753 through 775 )753 - 775112 - 134

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