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

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Basic information

Entry
Database: PDB / ID: 9hsv
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with (1H-pyrazol-3-yl)methanol
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~{H}-pyrazol-5-ylmethanol / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 (1H-pyrazol-3-yl)methanol
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)20,9414
Polymers20,6471
Non-polymers2943
Water2,576143
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8838
Polymers41,2942
Non-polymers5896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1930 Å2
ΔGint-8 kcal/mol
Surface area14060 Å2
Unit cell
Length a, b, c (Å)50.150, 71.112, 118.916
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-IRU / 1~{H}-pyrazol-5-ylmethanol


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


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
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: 1.55→61.03 Å / Num. obs: 43699 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.87 Å2 / CC1/2: 0.987 / Net I/σ(I): 8.6
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 1447 / CC1/2: 0.141

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→61.03 Å / SU ML: 0.2222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 2095 4.79 %
Rwork0.1979 41604 -
obs0.1989 43699 93.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.65 Å2
Refinement stepCycle: LAST / Resolution: 1.68→61.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 21 143 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611098
X-RAY DIFFRACTIONf_angle_d0.71471483
X-RAY DIFFRACTIONf_chiral_restr0.0542170
X-RAY DIFFRACTIONf_plane_restr0.0094182
X-RAY DIFFRACTIONf_dihedral_angle_d14.1123399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.30281420.30322809X-RAY DIFFRACTION95.07
1.72-1.760.32521490.28642844X-RAY DIFFRACTION95.14
1.76-1.810.29891390.25712804X-RAY DIFFRACTION94.24
1.81-1.860.2751640.24072820X-RAY DIFFRACTION94.31
1.86-1.920.2341300.23192736X-RAY DIFFRACTION92.6
1.92-1.990.22271530.23052764X-RAY DIFFRACTION92.84
1.99-2.070.21361350.21642771X-RAY DIFFRACTION93.92
2.07-2.170.21281400.19192854X-RAY DIFFRACTION94.9
2.17-2.280.24751440.20392769X-RAY DIFFRACTION93.67
2.28-2.420.22771420.20872740X-RAY DIFFRACTION92.91
2.42-2.610.22611290.19892760X-RAY DIFFRACTION92.18
2.61-2.870.23211170.20922800X-RAY DIFFRACTION93.43
2.87-3.290.19931640.18932708X-RAY DIFFRACTION92.29
3.29-4.140.2141360.17322704X-RAY DIFFRACTION90.53
4.14-61.030.18391110.16992721X-RAY DIFFRACTION90.33
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)
14.260057682250.4891564150531.335011555984.263569674350.04931233086123.278100923040.00719410820231-0.2110879481110.05036663296690.179671736246-0.02021930910150.118403788983-0.0241289902973-0.1074192469280.01460552639060.1035138537730.02684962297870.033691331940.14725888923-0.005895397267520.133125316271-4.93167524103-24.0543103234-23.8868169144
25.28904197717-5.22203879159-4.703963546795.259273653524.52465218465.683826648180.180287221461-0.4585430649220.003643565463511.01758658481-0.385844441770.762940021438-0.412589571551-0.4862430518690.05053239320660.395012182561-0.03951151156570.05046686757690.479733182187-0.04971171104080.3154674329921.86255308417-22.6104343517-9.69378149654
35.05429654558-0.1413697051521.559288377275.371811600480.43373758672.68279987117-0.0597927681626-0.130621064549-0.06350768037680.176274937356-0.0535344997543-0.137699636202-0.054428838464-0.006417906715050.08629472293230.105984471487-0.006799871208680.02422465666490.1503714038210.01545059674260.1209174691491.93941019471-23.746201853-23.2584578355
49.43253558732-0.3106117572770.7724443891237.016294157511.567011128283.57375975829-0.156110042411-0.1580955277650.4363458871260.2078327065460.050625250423-0.0874725485589-0.198187614870.1361599811260.07527255489320.1790986192670.0260462369589-0.05584265843560.1476144343250.007168496591580.212414224956-8.22430188475-13.9341685821-28.0458537673
55.701973748970.5647279887241.455178582038.18692875401-1.953593579685.68809796192-0.174161278575-0.1935905058390.2330162249290.3524166435720.07886515865090.15104945525-0.223146800730.02440598419030.08685920066610.187349152540.01600359384560.03994542849970.230267786056-0.01843095336590.231599057629-15.7689411123-13.9630137101-27.322611869
69.20377659857-4.15209923014.972445840987.29705468845-4.790310318683.93924577012-0.481257669762-1.58536835608-0.448257958531.063813220440.2098426125880.394637970607-0.116711299902-0.8242815738840.2151356491590.6501906904370.03985804519970.1788089445750.7502203740330.04268191453710.588717108281-12.7669072404-30.924523906-14.6482721846
74.691266151181.548781454510.4017624697481.72997527135-0.7074729938460.7772997671450.152052082139-0.7446552876510.04777398298891.34061651689-0.249827303988-0.94774176074-0.658583284954-0.1608465725570.02959634869360.789577451292-0.20616936193-0.04509151136160.676355389859-0.2197001232630.501577789529-5.38451187485-39.6017640745-2.87520490023
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 662 )616 - 6621 - 47
22chain 'A' and (resid 663 through 669 )663 - 66948 - 54
33chain 'A' and (resid 670 through 695 )670 - 69555 - 80
44chain 'A' and (resid 696 through 741 )696 - 74181 - 99
55chain 'A' and (resid 742 through 753 )742 - 753100 - 111
66chain 'A' and (resid 754 through 760 )754 - 760112 - 118
77chain 'A' and (resid 761 through 774 )761 - 772119 - 130

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