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

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Basic information

Entry
Database: PDB / ID: 9hsf
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-carbamimidoylacetamide
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: 2.1 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 2-carbamimidoylacetamide
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)20,9112
Polymers20,8101
Non-polymers1011
Water86548
1
A: Cholinephosphate cytidylyltransferase
hetero molecules

A: Cholinephosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8224
Polymers41,6202
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2220 Å2
ΔGint-7 kcal/mol
Surface area14280 Å2
Unit cell
Length a, b, c (Å)50.004, 68.023, 116.315
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
Components on special symmetry positions
IDModelComponents
11A-921-

HOH

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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-A1IWT / 3-azanyl-3-azanylidene-propanamide


Mass: 101.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
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: ID30B / Wavelength: 0.965459 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.9→34.01 Å / Num. obs: 19598 / % possible obs: 94.99 % / Redundancy: 3.7 % / Biso Wilson estimate: 41 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.4
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 729 / CC1/2: 0.869

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.01 Å / SU ML: 0.4336 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.6493
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2871 989 5.05 %
Rwork0.2349 18609 -
obs0.2374 19598 87.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 7 48 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731069
X-RAY DIFFRACTIONf_angle_d0.84331450
X-RAY DIFFRACTIONf_chiral_restr0.0517169
X-RAY DIFFRACTIONf_plane_restr0.0127181
X-RAY DIFFRACTIONf_dihedral_angle_d15.8141384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.40731300.37372743X-RAY DIFFRACTION90.29
2.21-2.350.39651290.40432416X-RAY DIFFRACTION79.56
2.35-2.530.34461570.28822751X-RAY DIFFRACTION90.82
2.53-2.780.34481460.29232676X-RAY DIFFRACTION88.13
2.79-3.190.29821440.25832701X-RAY DIFFRACTION89.55
3.19-4.020.26161430.20832687X-RAY DIFFRACTION87.75
4.02-34.010.24171400.1782635X-RAY DIFFRACTION86.77
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)
14.80372356795-0.783685075486-2.161801985394.172746484282.497769514932.415009487210.00236210176331-0.182769854247-0.1166204506870.23167278404-0.04890336717120.1004285367740.4485605489820.2197177822260.0825210756320.4522830327050.0298260830627-0.03059307188670.275459734380.04810530444480.224011682353-18.0756907502-7.77650979284-23.1996660847
23.294321460170.678317694667-3.51571782145.721639673570.819599405324.195546957870.0646298022570.8162613071550.442536621761-1.227324014160.305489641489-0.261707436024-0.252713207229-0.30941086616-0.3735569736580.5473825675760.00521236738727-0.02428276092830.4038597786270.04413068790740.361044586029-17.638321979-10.5607339964-31.7691891528
33.723019127360.000303239205813-0.9555374344494.107301005250.4128911989872.19160057804-0.325674097843-0.101963360682-0.3984028166570.2019365262980.08331800975220.03333184309140.5990982400590.1375009311140.2365181046470.5523942079720.0166656583707-0.01840083148030.264862570350.02291996633730.301615876119-25.0730432501-15.3166177818-19.9935225414
48.70590724457-0.9048438822063.409896702823.65531162018-3.325291688274.89319883616-0.054612761893-0.00640793856724-0.4319052872690.197726972778-0.2331895546810.1897922925160.8268360134340.04848600951780.4051769947160.7216852113640.02557776702710.04596939775880.405861179092-0.01165545793890.358375956282-11.0158319405-20.0013394974-27.4541038642
52.62480917346-1.16548206922-2.321849429491.55362385321.7669385372.5794729750.161413757428-0.435288330237-0.2312457234130.0986636746625-0.3386013777710.123923995878-0.7198219468330.7112626418630.05197323830240.682730519601-0.094713507118-0.002337527676410.615812561710.04726158389540.415458069096-16.65520107522.11447936161-4.82826209544
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 642 )617 - 6421 - 26
22chain 'A' and (resid 643 through 653 )643 - 65327 - 37
33chain 'A' and (resid 654 through 701 )654 - 70138 - 85
44chain 'A' and (resid 702 through 752 )702 - 75286 - 108
55chain 'A' and (resid 753 through 775 )753 - 775109 - 131

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