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

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Basic information

Entry
Database: PDB / ID: 9hsz
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 4-aminopyridine
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
4-AMINOPYRIDINE / 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 4-aminopyridine
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)21,0275
Polymers20,6471
Non-polymers3804
Water1,31573
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,05510
Polymers41,2942
Non-polymers7618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area3640 Å2
ΔGint18 kcal/mol
Surface area14500 Å2
Unit cell
Length a, b, c (Å)50.133, 70.736, 119.057
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-4AP / 4-AMINOPYRIDINE


Mass: 95.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H7N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
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-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.96→60.81 Å / Num. obs: 28204 / % possible obs: 98.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 43.77 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.044 / Rrim(I) all: 0.102 / Χ2: 0.85 / Net I/σ(I): 8.8
Reflection shellResolution: 1.96→2.01 Å / % possible obs: 98.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.99 / Num. measured all: 5202 / Num. unique obs: 1066 / CC1/2: 0.53 / Rpim(I) all: 0.482 / Rrim(I) all: 1.106 / Χ2: 0.66 / Net I/σ(I) obs: 1.1

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→60.81 Å / SU ML: 0.2529 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 1389 4.92 %
Rwork0.1998 26815 -
obs0.2008 28204 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.91 Å2
Refinement stepCycle: LAST / Resolution: 1.96→60.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 28 73 1138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651085
X-RAY DIFFRACTIONf_angle_d0.69491465
X-RAY DIFFRACTIONf_chiral_restr0.0539168
X-RAY DIFFRACTIONf_plane_restr0.0049181
X-RAY DIFFRACTIONf_dihedral_angle_d13.8994381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.030.32981570.30532634X-RAY DIFFRACTION95.22
2.03-2.110.29791520.25932701X-RAY DIFFRACTION96.32
2.11-2.210.26561220.2492697X-RAY DIFFRACTION96.41
2.21-2.320.26711250.22742704X-RAY DIFFRACTION96.36
2.32-2.470.221510.22472679X-RAY DIFFRACTION96.19
2.47-2.660.24981140.21262691X-RAY DIFFRACTION95.93
2.66-2.930.22981500.24222696X-RAY DIFFRACTION95.66
2.93-3.350.25811460.20962681X-RAY DIFFRACTION96.16
3.35-4.220.16771480.182654X-RAY DIFFRACTION96.26
4.22-60.810.21641240.17062678X-RAY DIFFRACTION94.28
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)
15.843988118370.1094122773481.105426771764.4481516297-0.8461283412853.3101734670.0523693661276-0.283958476640.2943521364070.300740358481-0.110671917721-0.00593374246886-0.1941219945470.01999580013750.06190582243390.249123643129-0.007327558205890.04040461388350.318942069438-0.05628052459760.304202648351-2.79696642481-22.1845119132-24.0229020572
22.28736651612-2.485595948460.4687285322614.397701152350.0609905060272.05413094363-0.6941392894-1.948990469490.2726693824922.915761361840.2650182530540.258751966859-0.817429329566-0.3090174671160.500878551760.8464772699530.1106259805170.1019610609250.836686030183-0.1121628654160.479986217824-14.4324987874-17.3140688662-21.4792591367
31.82907147789-1.859744584862.742887709244.06208409324-4.265597538165.08259982119-0.256260706304-0.5080003053290.2404391079680.6102610471460.307753306660.00748497182984-0.0520687690341-0.668415230822-0.1205119652990.6238149858610.01460670571140.09354927765030.659999529041-0.1569621818080.437889529929-11.4250141382-27.261134445-15.3047512383
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 706 )616 - 7061 - 91
22chain 'A' and (resid 707 through 741 )707 - 74192 - 99
33chain 'A' and (resid 742 through 772 )742 - 772100 - 130

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