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- PDB-4iv8: Crystal structure of N-methyl transferase from Plasmodium knowles... -

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Basic information

Entry
Database: PDB / ID: 4iv8
TitleCrystal structure of N-methyl transferase from Plasmodium knowlesi complexed with S-adenosyl methionine
ComponentsPhosphoethanolamine N-methyltransferase,putative
KeywordsTRANSFERASE / AdoMet_MTase
Function / homology
Function and homology information


phosphoethanolamine N-methyltransferase activity / phosphoethanolamine N-methyltransferase / methylation
Similarity search - Function
Methyltransferase type 11 / 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
BETA-MERCAPTOETHANOL / S-ADENOSYLMETHIONINE / Phosphoethanolamine N-methyltransferase / Phosphoethanolamine N-methyltransferase
Similarity search - Component
Biological speciesPlasmodium knowlesi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLukk, T. / Nair, S.K.
CitationJournal: To be Published
Title: Phosphoethanolamine N-methyl transferase is a Malarial drug target.
Authors: Lukk, T. / Nair, S.K.
History
DepositionJan 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Phosphoethanolamine N-methyltransferase,putative
B: Phosphoethanolamine N-methyltransferase,putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3296
Polymers66,3762
Non-polymers9534
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-18 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.710, 96.760, 38.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphoethanolamine N-methyltransferase,putative


Mass: 33187.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Strain: H / Gene: PKH_121150 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B3L8G9, UniProt: A0A384KJX3*PLUS, phosphoethanolamine N-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein solution was at 15 mg/mL containing 20 mM Tris, 100 mM NaCl, 2 mM EDTA and 5 mM bME, 5 mM SAM. Mother liqueur contained 0.1 M Na-acetate (pH 5.0) and 20% PEG 3.350. Cryoprotectant ...Details: Protein solution was at 15 mg/mL containing 20 mM Tris, 100 mM NaCl, 2 mM EDTA and 5 mM bME, 5 mM SAM. Mother liqueur contained 0.1 M Na-acetate (pH 5.0) and 20% PEG 3.350. Cryoprotectant was 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 15, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 51102 / Num. obs: 51018 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.857 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.81
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.950.7482.562655236791100
1.95-20.5333.542635636491100
2-2.060.4334.342535235191100
2.06-2.120.3595.192497834601100
2.12-2.190.296.252358532711100
2.19-2.270.237.612353932651100
2.27-2.360.1889.112227430931100
2.36-2.450.1719.692158130001100
2.45-2.560.14411.292106429241100
2.56-2.690.12112.97195622733199.9
2.69-2.830.10214.98186942629199.9
2.83-30.08417.381785425151100
3-3.210.07119.911671623701100
3.21-3.470.05623.681537221981100
3.47-3.80.05326.341404420301100
3.8-4.250.04828.071286218691100
4.25-4.910.04530112131652199.9
4.91-6.010.04628.0895631412199.9
6.01-8.50.04527.9740811301100
8.5-200.04828.733549620189.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UJ7

3uj7


Resolution: 1.9→19.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2626 / WRfactor Rwork: 0.2271 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7511 / SU B: 3.953 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1732 / SU Rfree: 0.1597 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 2549 5 %RANDOM
Rwork0.2328 ---
all0.253 51016 --
obs0.2347 50979 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.28 Å2 / Biso mean: 27.0975 Å2 / Biso min: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 62 363 4473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024220
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9895674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76225.313192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93815818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.741510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023100
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 170 -
Rwork0.295 3210 -
all-3380 -
obs--99.97 %

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