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

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Basic information

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


methyltransferase activity / methylation
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
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / Phosphoethanolamine N-methyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.466 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

Downloads & links

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Assembly

Deposited unit
A: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2252
Polymers31,0841
Non-polymers1411
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.664, 44.075, 77.053
Angle α, β, γ (deg.)90.00, 108.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-275-

HOH

21A-405-

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-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID / Phosphorylethanolamine


Mass: 141.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H8NO4P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 47.01 %
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: 1.466→32.5 Å / Num. obs: 48655 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.063 / Net I/σ(I): 31.3
Reflection shellResolution: 1.47→1.5 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.406 / % possible all: 94.2

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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: 1.466→32.495 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 2459 5.06 %random
Rwork0.1653 ---
obs0.166 48642 99.05 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.397 Å2 / ksol: 0.407 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0579 Å2-0 Å2-1.7334 Å2
2---6.8492 Å2-0 Å2
3---1.7912 Å2
Refinement stepCycle: LAST / Resolution: 1.466→32.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 8 390 2516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062214
X-RAY DIFFRACTIONf_angle_d0.9662992
X-RAY DIFFRACTIONf_dihedral_angle_d11.563842
X-RAY DIFFRACTIONf_chiral_restr0.07320
X-RAY DIFFRACTIONf_plane_restr0.004381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4665-1.51890.29412270.28854367X-RAY DIFFRACTION94
1.5189-1.57970.28112130.23874656X-RAY DIFFRACTION100
1.5797-1.65160.25922460.20344631X-RAY DIFFRACTION100
1.6516-1.73870.21922360.18744650X-RAY DIFFRACTION100
1.7387-1.84760.20292650.1754627X-RAY DIFFRACTION100
1.8476-1.99030.2062560.16334617X-RAY DIFFRACTION100
1.9903-2.19050.1692490.16174666X-RAY DIFFRACTION100
2.1905-2.50740.16152730.1544628X-RAY DIFFRACTION100
2.5074-3.15860.17542490.16094700X-RAY DIFFRACTION100
3.1586-32.50260.1482450.1484641X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 19.439 Å / Origin y: 19.4233 Å / Origin z: 19.9745 Å
111213212223313233
T0.1489 Å20.0116 Å2-0.0218 Å2-0.1348 Å2-0.0033 Å2--0.0852 Å2
L0.4218 °20.1895 °2-0.1527 °2-0.8389 °20.11 °2--0.2502 °2
S-0.0234 Å °0.0275 Å °0.0099 Å °-0.1506 Å °-0.0076 Å °0.0553 Å °-0.0347 Å °0.0288 Å °0.0256 Å °
Refinement TLS groupSelection details: chain A

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