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- PDB-3uj7: Phosphoethanolamine methyltransferase from Plasmodium falciparum ... -

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Basic information

Entry
Database: PDB / ID: 3uj7
TitlePhosphoethanolamine methyltransferase from Plasmodium falciparum in complex with SAM and PO4
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
PHOSPHATE ION / S-ADENOSYLMETHIONINE / Phosphoethanolamine N-methyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 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)63,1556
Polymers62,1682
Non-polymers9874
Water15,331851
1
A: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5783
Polymers31,0841
Non-polymers4932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5783
Polymers31,0841
Non-polymers4932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.035, 44.130, 88.411
Angle α, β, γ (deg.)90.00, 108.48, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

21B-585-

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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
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: 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: 1.549→37.8 Å / Num. obs: 74087 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.067 / Net I/σ(I): 18.1
Reflection shellResolution: 1.55→1.6 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.382 / % possible all: 99.1

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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: 1.549→37.774 Å / SU ML: 0.17 / σ(F): 0.03 / Phase error: 18.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 3724 5.03 %Random
Rwork0.1665 ---
obs0.1674 74087 89.83 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.248 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.5601 Å2
2--0.0167 Å2-0 Å2
3----0.3867 Å2
Refinement stepCycle: LAST / Resolution: 1.549→37.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 64 851 5171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064543
X-RAY DIFFRACTIONf_angle_d1.036148
X-RAY DIFFRACTIONf_dihedral_angle_d13.3561726
X-RAY DIFFRACTIONf_chiral_restr0.074653
X-RAY DIFFRACTIONf_plane_restr0.004782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5489-1.60430.28363010.2365784X-RAY DIFFRACTION74
1.6043-1.66850.21353470.19196553X-RAY DIFFRACTION84
1.6685-1.74440.2183720.19086764X-RAY DIFFRACTION87
1.7444-1.83640.21783770.17446970X-RAY DIFFRACTION89
1.8364-1.95150.19523720.16437181X-RAY DIFFRACTION93
1.9515-2.10210.1864180.16617341X-RAY DIFFRACTION94
2.1021-2.31360.1783680.15747410X-RAY DIFFRACTION95
2.3136-2.64840.1943890.16387447X-RAY DIFFRACTION95
2.6484-3.33630.17743810.1657461X-RAY DIFFRACTION94
3.3363-37.78550.15383990.15457452X-RAY DIFFRACTION92
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)
10.3113-0.0567-0.09970.4265-0.08660.38180.01090.01130.00120.002-0.00350.0240.0062-0.0116-0.00760.0356-0.0018-0.00830.0458-0.00060.04211.9981-20.49225.0227
20.38210.0503-0.06990.54750.00110.42080.0199-0.01790.00680.0095-0.0036-0.0251-0.03850.0199-0.01470.0435-0.0044-0.00420.0513-0.00650.047949.15391.329217.8809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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