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- PDB-3ujd: Phosphoethanolamine methyltransferase mutant (Y19F) from Plasmodi... -

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Basic information

Entry
Database: PDB / ID: 3ujd
TitlePhosphoethanolamine methyltransferase mutant (Y19F) 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: 1.5 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)31,2522
Polymers31,0681
Non-polymers1841
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.227, 44.064, 76.974
Angle α, β, γ (deg.)90.00, 108.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

21A-333-

HOH

31A-379-

HOH

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Components

#1: Protein Phosphoethanolamine N-methyltransferase


Mass: 31068.121 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.: 365 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 277 K / 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 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: 1.496→43 Å / Num. obs: 45420 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.06 / Net I/σ(I): 26.2
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.504 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→42.99 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 16.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 2304 5.08 %
Rwork0.162 --
obs0.163 45391 98.6 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.2 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0024 Å2-0 Å21.4327 Å2
2---0.9443 Å2-0 Å2
3---0.9419 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 11 365 2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062239
X-RAY DIFFRACTIONf_angle_d0.9753036
X-RAY DIFFRACTIONf_dihedral_angle_d11.404858
X-RAY DIFFRACTIONf_chiral_restr0.071327
X-RAY DIFFRACTIONf_plane_restr0.004385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4962-1.54970.26992290.26473942X-RAY DIFFRACTION91
1.5497-1.61170.27372320.21914317X-RAY DIFFRACTION100
1.6117-1.68510.21742410.19414304X-RAY DIFFRACTION100
1.6851-1.77390.22642230.17524374X-RAY DIFFRACTION100
1.7739-1.88510.19242150.16044338X-RAY DIFFRACTION100
1.8851-2.03060.19582330.15224327X-RAY DIFFRACTION100
2.0306-2.23490.1692490.15294317X-RAY DIFFRACTION99
2.2349-2.55830.1762130.15214370X-RAY DIFFRACTION99
2.5583-3.2230.17252210.1564374X-RAY DIFFRACTION99
3.223-43.00340.16552480.15434424X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.3901 Å / Origin y: 19.9533 Å / Origin z: 19.8604 Å
111213212223313233
T0.1086 Å20.0089 Å2-0.017 Å2-0.108 Å20.0021 Å2--0.0744 Å2
L0.4617 °20.2496 °2-0.098 °2-0.7781 °20.1384 °2--0.2321 °2
S-0.0123 Å °0.0203 Å °-0.0043 Å °-0.0403 Å °0.002 Å °-0.0013 Å °-0.007 Å °-0.0245 Å °0.009 Å °
Refinement TLS groupSelection details: chain A

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