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- PDB-8ys9: Crystal structure of Phosphatidylethanolamine N-methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 8ys9
TitleCrystal structure of Phosphatidylethanolamine N-methyltransferase from R. thermophilum complexed with DMPE and SAH
ComponentsPhosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase
KeywordsTRANSFERASE / Phosphatidylethanolamine / Phosphatidylcholine / Bacterial phosphatidylcholine biosynthesis / Peripheral membrane protein / SAM-dependent methyltransferase / MEMBRANE PROTEIN / PmtA
Function / homology
Function and homology information


phosphatidylethanolamine N-methyltransferase / phosphatidyl-N-methylethanolamine N-methyltransferase / phosphatidylethanolamine N-methyltransferase activity / : / phosphatidyl-N-methylethanolamine N-methyltransferase activity / methylation
Similarity search - Function
: / Methyltransferase type 11 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / L(+)-TARTARIC ACID / Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesRubellimicrobium thermophilum DSM 16684 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsKim, J. / Salsabila, S.D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Sci Adv / Year: 2024
Title: Structural insights into phosphatidylethanolamine N -methyltransferase PmtA mediating bacterial phosphatidylcholine synthesis.
Authors: Salsabila, S.D. / Kim, J.
History
DepositionMar 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase
B: Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6999
Polymers48,3062
Non-polymers2,3947
Water6,053336
1
A: Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4054
Polymers24,1531
Non-polymers1,2533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2945
Polymers24,1531
Non-polymers1,1414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.042, 77.681, 83.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase


Mass: 24152.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubellimicrobium thermophilum DSM 16684 (bacteria)
Gene: ruthe_01610 / Plasmid: pLATE31 / Details (production host): C-terminal Histag / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: S9SHS0, phosphatidylethanolamine N-methyltransferase, phosphatidyl-N-methylethanolamine N-methyltransferase
#6: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 342 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1L1H / [(2~{R})-3-[2-(dimethylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-[(~{Z})-octadec-9-enoyl]oxy-propyl] (~{Z})-octadec-9-enoate


Mass: 772.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H82NO8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 48.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4 M ammonium sulfate, 0.1 M potassium sodium tartrate tetrahydrate, 20% (v/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.46→56.77 Å / Num. obs: 79982 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 1 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.029 / Rrim(I) all: 0.109 / Net I/σ(I): 13.2
Reflection shellResolution: 1.463→1.488 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3943 / CC1/2: 0.322 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata processing
MOLREPphasing
Cootmodel building
MxDCdata collection
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→56.77 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.691 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3983 4.99 %RANDOM
Rwork0.152 ---
obs-79830 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0 Å2
2---0.4 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.46→56.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 160 336 3735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163415
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.8694683
X-RAY DIFFRACTIONr_angle_other_deg0.6231.767806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5025413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.75565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84610546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02840
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.5082.241667
X-RAY DIFFRACTIONr_mcbond_other6.5012.241667
X-RAY DIFFRACTIONr_mcangle_it8.5844.0382075
X-RAY DIFFRACTIONr_mcangle_other8.5824.0372076
X-RAY DIFFRACTIONr_scbond_it9.252.7121796
X-RAY DIFFRACTIONr_scbond_other9.2172.7131789
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.9544.7692597
X-RAY DIFFRACTIONr_long_range_B_refined16.26226.033701
X-RAY DIFFRACTIONr_long_range_B_other15.67824.463622
X-RAY DIFFRACTIONr_rigid_bond_restr4.59436878
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.463→1.501 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 277 -
Rwork0.325 5428 -
obs--97.76 %

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