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- PDB-3uj9: Phosphoethanolamine methyltransferase from Plasmodium falciparum ... -

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Basic information

Entry
Database: PDB / ID: 3uj9
TitlePhosphoethanolamine methyltransferase from Plasmodium falciparum in complex with phosphocholine
ComponentsPhosphoethanolamine N-methyltransferase
KeywordsTRANSFERASE / Plasmodium / parasite / methyltransferase
Function / homology
Function and homology information


phosphoethanolamine N-methyltransferase activity / : / phosphoethanolamine N-methyltransferase / phosphatidylcholine biosynthetic process / methylation / Golgi membrane / Golgi apparatus
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOCHOLINE / Phosphoethanolamine N-methyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsLee, S.G. / Kim, Y. / Alpert, T.D. / Nagata, A. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure and reaction mechanism of phosphoethanolamine methyltransferase from the malaria parasite Plasmodium falciparum: an antiparasitic drug target.
Authors: Lee, S.G. / Kim, Y. / Alpert, T.D. / Nagata, A. / Jez, J.M.
History
DepositionNov 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Atomic model / Other
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2682
Polymers31,0841
Non-polymers1841
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.077, 43.982, 77.032
Angle α, β, γ (deg.)90.00, 109.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

21A-353-

HOH

31A-525-

HOH

41A-726-

HOH

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Components

#1: Protein Phosphoethanolamine N-methyltransferase


Mass: 31084.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PMT / Production host: Escherichia coli (E. coli) / References: UniProt: Q6T755
#2: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG-8000, 0.1 M sodium cacodylate, pH 6.5, 0.2 M sodium acetate, 5 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.24→24.9 Å / Num. obs: 76023 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.078 / Net I/σ(I): 29.3
Reflection shellResolution: 1.24→1.26 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.359 / % possible all: 88.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→24.866 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 15.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 3827 5.05 %random
Rwork0.1474 ---
obs0.1487 75716 93.64 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.63 Å2 / ksol: 0.422 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0125 Å2-0 Å2-0.5712 Å2
2---3.9616 Å2-0 Å2
3---2.9491 Å2
Refinement stepCycle: LAST / Resolution: 1.24→24.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 11 493 2628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052295
X-RAY DIFFRACTIONf_angle_d0.9473109
X-RAY DIFFRACTIONf_dihedral_angle_d11.478878
X-RAY DIFFRACTIONf_chiral_restr0.069329
X-RAY DIFFRACTIONf_plane_restr0.004399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2404-1.25610.30911240.2592343X-RAY DIFFRACTION81
1.2561-1.27260.29131240.25162529X-RAY DIFFRACTION90
1.2726-1.290.27711530.23212608X-RAY DIFFRACTION92
1.29-1.30850.26161420.21432568X-RAY DIFFRACTION92
1.3085-1.3280.25021410.20512602X-RAY DIFFRACTION92
1.328-1.34880.25941440.18352539X-RAY DIFFRACTION91
1.3488-1.37090.18121470.17042598X-RAY DIFFRACTION91
1.3709-1.39450.23061360.16482618X-RAY DIFFRACTION92
1.3945-1.41990.21531350.15082596X-RAY DIFFRACTION93
1.4199-1.44720.1841380.14172599X-RAY DIFFRACTION92
1.4472-1.47670.15791400.12682691X-RAY DIFFRACTION93
1.4767-1.50880.15821550.12062606X-RAY DIFFRACTION94
1.5088-1.54390.16831090.12132677X-RAY DIFFRACTION94
1.5439-1.58250.15381660.12412631X-RAY DIFFRACTION94
1.5825-1.62530.17431520.12082693X-RAY DIFFRACTION94
1.6253-1.67310.15731530.12312709X-RAY DIFFRACTION95
1.6731-1.72710.15841550.1242648X-RAY DIFFRACTION95
1.7271-1.78880.16751550.12892702X-RAY DIFFRACTION96
1.7888-1.86040.16681640.12852712X-RAY DIFFRACTION96
1.8604-1.9450.16671330.13752729X-RAY DIFFRACTION96
1.945-2.04750.1681350.1392764X-RAY DIFFRACTION96
2.0475-2.17570.17311120.13952788X-RAY DIFFRACTION97
2.1757-2.34360.13211460.13432765X-RAY DIFFRACTION97
2.3436-2.57920.17421530.14282795X-RAY DIFFRACTION97
2.5792-2.9520.15281340.14772838X-RAY DIFFRACTION98
2.952-3.71720.17211270.14142825X-RAY DIFFRACTION98
3.7172-24.8710.17241540.172716X-RAY DIFFRACTION92

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