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Yorodumi- PDB-8ys9: Crystal structure of Phosphatidylethanolamine N-methyltransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ys9 | ||||||
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Title | Crystal structure of Phosphatidylethanolamine N-methyltransferase from R. thermophilum complexed with DMPE and SAH | ||||||
Components | Phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / 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 | ||||||
Biological species | Rubellimicrobium thermophilum DSM 16684 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Kim, J. / Salsabila, S.D. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structural insights into phosphatidylethanolamine N -methyltransferase PmtA mediating bacterial phosphatidylcholine synthesis. Authors: Salsabila, S.D. / Kim, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ys9.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ys9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ys9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ys9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8ys9_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8ys9_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 8ys9_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/8ys9 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/8ys9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | 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 / | |
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-Non-polymers , 5 types, 342 molecules
#2: Chemical | #3: Chemical | ChemComp-A1L1H / [( | Mass: 772.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H82NO8P / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | #5: Chemical | ChemComp-TLA / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.38 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2
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Refinement step | Cycle: 1 / Resolution: 1.46→56.77 Å
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