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- PDB-3uj6: SeMet Phosphoethanolamine methyltransferase from Plasmodium falci... -

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Basic information

Entry
Database: PDB / ID: 3uj6
TitleSeMet Phosphoethanolamine methyltransferase from Plasmodium falciparum in complex with SAM and PO4
ComponentsPhosphoethanolamine N-methyltransferase
KeywordsTRANSFERASE / Plasmodium / parasite / methyltransferase
Function / homology
Function and homology information


phosphomethylethanolamine N-methyltransferase activity / 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
PHOSPHATE ION / S-ADENOSYLMETHIONINE / Phosphoethanolamine N-methyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.974 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7653
Polymers31,2721
Non-polymers4932
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.388, 44.151, 77.064
Angle α, β, γ (deg.)90.00, 108.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-529-

HOH

31A-578-

HOH

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Components

#1: Protein Phosphoethanolamine N-methyltransferase /


Mass: 31271.703 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-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG-8000, 0.1 M sodium cacodylate, 0.2 M sodium acetate, 20 mM tris(2-carboxyethyl)phosphine (TCEP), pH 6.5, 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: Nov 22, 2010
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: 1.97→36.518 Å / Num. obs: 19867 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.063 / Net I/σ(I): 25.2
Reflection shellResolution: 1.97→2 Å / Mean I/σ(I) obs: 11.1 / Rsym value: 0.107 / % possible all: 67.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.974→36.518 Å / SU ML: 0.19 / σ(F): 0.28 / Phase error: 16.63 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 1987 10 %random
Rwork0.1491 ---
obs0.1527 19867 97.92 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.692 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8459 Å2-0 Å2-0.4148 Å2
2---4.2817 Å2-0 Å2
3---1.4358 Å2
Refinement stepCycle: LAST / Resolution: 1.974→36.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 32 322 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062220
X-RAY DIFFRACTIONf_angle_d1.0152996
X-RAY DIFFRACTIONf_dihedral_angle_d13.704834
X-RAY DIFFRACTIONf_chiral_restr0.073318
X-RAY DIFFRACTIONf_plane_restr0.003379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9738-2.04440.20221790.1421611X-RAY DIFFRACTION90
2.0444-2.12620.20261980.14211781X-RAY DIFFRACTION98
2.1262-2.2230.20231990.13721795X-RAY DIFFRACTION99
2.223-2.34020.18412020.13971814X-RAY DIFFRACTION99
2.3402-2.48670.20461980.1471783X-RAY DIFFRACTION99
2.4867-2.67870.18192010.15521803X-RAY DIFFRACTION100
2.6787-2.94810.19512030.15461826X-RAY DIFFRACTION100
2.9481-3.37450.20622010.15881813X-RAY DIFFRACTION100
3.3745-4.25050.14642020.14021823X-RAY DIFFRACTION99
4.2505-36.52410.18182040.15891831X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 19.4151 Å / Origin y: 20.6989 Å / Origin z: 19.8324 Å
111213212223313233
T0.0417 Å20.0148 Å2-0.0041 Å2-0.0526 Å2-0.0016 Å2--0.0419 Å2
L0.4413 °20.1893 °2-0.0953 °2-0.6645 °20.0021 °2--0.3927 °2
S-0.0131 Å °-0.0015 Å °-0.0162 Å °-0.0411 Å °-0.0013 Å °0.0144 Å °-0.0104 Å °-0.0339 Å °0.0114 Å °
Refinement TLS groupSelection details: chain A

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