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

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Basic information

Entry
Database: PDB / ID: 3ujb
TitlePhosphoethanolamine methyltransferase from Plasmodium falciparum in complex with SAH and phosphoethanolamine
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
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: 1.521 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
B: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2196
Polymers62,1682
Non-polymers1,0514
Water14,268792
1
A: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6103
Polymers31,0841
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)31,6103
Polymers31,0841
Non-polymers5252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.804, 44.158, 88.991
Angle α, β, γ (deg.)90.00, 108.31, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-269-

HOH

21A-379-

HOH

31A-626-

HOH

41B-268-

HOH

51B-365-

HOH

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Components

#1: Protein Phosphoethanolamine N-methyltransferase


Mass: 31084.121 Da / Num. of mol.: 2
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


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.: 792 / 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: 46.63 %
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: 1.52→38.112 Å / Num. obs: 87067 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.082 / Net I/σ(I): 19.9
Reflection shellResolution: 1.52→1.55 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.638 / % possible all: 99.2

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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: 1.521→38.112 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 4354 5.02 %random
Rwork0.1716 ---
obs0.1728 86729 99.08 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.671 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0331 Å2-0 Å2-1.4775 Å2
2---3.7681 Å2-0 Å2
3---3.8012 Å2
Refinement stepCycle: LAST / Resolution: 1.521→38.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 68 792 5080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064458
X-RAY DIFFRACTIONf_angle_d1.0166026
X-RAY DIFFRACTIONf_dihedral_angle_d17.0481738
X-RAY DIFFRACTIONf_chiral_restr0.074643
X-RAY DIFFRACTIONf_plane_restr0.004762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5207-1.57510.28464210.25277924X-RAY DIFFRACTION96
1.5751-1.63820.26134380.22358125X-RAY DIFFRACTION99
1.6382-1.71270.23224210.19528202X-RAY DIFFRACTION99
1.7127-1.8030.21074280.18298189X-RAY DIFFRACTION100
1.803-1.9160.21474400.16868294X-RAY DIFFRACTION100
1.916-2.06390.20014320.16868243X-RAY DIFFRACTION100
2.0639-2.27160.17554500.16428292X-RAY DIFFRACTION100
2.2716-2.60020.19594530.1648311X-RAY DIFFRACTION100
2.6002-3.27570.19264530.16628314X-RAY DIFFRACTION100
3.2757-38.12380.17134180.15738481X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4393-0.01960.05450.52-0.09460.34160.02330.00610.0189-0.0603-0.0110.04530.0003-0.0183-0.00990.0630.00160.00420.0632-0.00040.053750.74810.531324.9569
20.5661-0.0362-0.10250.5604-0.11810.37810.0120.01850.0017-0.05590.01260.0657-0.0033-0.0236-0.02470.0727-0.0012-0.00570.07050.00150.064437.798122.770466.4409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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