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- PDB-4r6x: Plasmodium falciparum phosphoethanolamine methyltransferase D128A... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4r6x
TitlePlasmodium falciparum phosphoethanolamine methyltransferase D128A mutant in complex with S-adenosylhomocysteine and phosphoethanolamine
ComponentsPhosphoethanolamine N-methyltransferase
KeywordsTRANSFERASE / 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
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / S-ADENOSYL-L-HOMOCYSTEINE / Phosphoethanolamine N-methyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5534 Å
AuthorsLee, S.G. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: An Alternative Mechanism for the Methylation of Phosphoethanolamine Catalyzed by Plasmodium falciparum Phosphoethanolamine Methyltransferase.
Authors: Saen-Oon, S. / Lee, S.G. / Jez, J.M. / Guallar, V.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2736
Polymers60,2222
Non-polymers1,0514
Water2,432135
1
A: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6363
Polymers30,1111
Non-polymers5252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6363
Polymers30,1111
Non-polymers5252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.826, 43.652, 88.053
Angle α, β, γ (deg.)90.00, 107.79, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Phosphoethanolamine N-methyltransferase


Mass: 30111.012 Da / Num. of mol.: 2 / Mutation: D128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PMT / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6T755
#2: Chemical ChemComp-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID


Mass: 141.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8NO4P
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growDetails: 20% PEG-8000, 0.1 M sodium cacodylate, pH 6.5, 0.2 M sodium acetate, 20 mM tris(2-carboxyethyl)phosphine, 5 mM SAH, and 5 mM pEA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.553→38.719 Å / Num. all: 18462 / Num. obs: 17323 / % possible obs: 93.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3UJ7

3uj7


Resolution: 2.5534→38.719 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 887 5.12 %random
Rwork0.2027 ---
obs0.2054 17323 93.83 %-
all-18462 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5534→38.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4242 0 68 135 4445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024481
X-RAY DIFFRACTIONf_angle_d0.5856054
X-RAY DIFFRACTIONf_dihedral_angle_d16.0861743
X-RAY DIFFRACTIONf_chiral_restr0.045647
X-RAY DIFFRACTIONf_plane_restr0.002763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5534-2.71340.30441020.25051943X-RAY DIFFRACTION67
2.7134-2.92280.32391480.24182880X-RAY DIFFRACTION100
2.9228-3.21680.29061590.22422857X-RAY DIFFRACTION99
3.2168-3.6820.2831480.20832894X-RAY DIFFRACTION99
3.682-4.63760.20951550.17552905X-RAY DIFFRACTION99
4.6376-38.72320.23111750.1842957X-RAY DIFFRACTION99

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