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Yorodumi- PDB-6vd1: Crystal structure of Arabidopsis thaliana S-adenosylmethionine Sy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vd1 | ||||||
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Title | Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with S-adenosylmethionine and PPNP | ||||||
Components | S-adenosylmethionine synthase 2 | ||||||
Keywords | TRANSFERASE / methionine adenosyltransferase / SAM synthase | ||||||
Function / homology | Function and homology information plant-type cell wall / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / plasmodesma / one-carbon metabolic process / copper ion binding / nucleolus / extracellular exosome / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Sekula, B. / Ruszkowski, M. / Dauter, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2020 Title: S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. Authors: Sekula, B. / Ruszkowski, M. / Dauter, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vd1.cif.gz | 385.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vd1.ent.gz | 304.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/6vd1 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vd1 | HTTPS FTP |
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-Related structure data
Related structure data | 6vcwC 6vcxC 6vcyC 6vczSC 6vd0C 6vd2C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44169.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: leaves / Gene: SAM2, At4g01850, T7B11.11 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17562, methionine adenosyltransferase |
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-Non-polymers , 12 types, 1218 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-1PE / | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-PDO / | #11: Chemical | ChemComp-PGR / | #12: Chemical | ChemComp-PE8 / | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.12 M Alcohols (1,6-hexanediol; 1-butanol; 1,2-propanediol; 2-propanol; 1,4-butanediol; 1,3-propanediol), 0.1 M HEPES and MOPS buffer at pH 7.5, 20% mmPEG500, 10% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 17, 2018 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→47.09 Å / Num. obs: 232535 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.35 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.45 |
Reflection shell | Resolution: 1.32→1.4 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 37677 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VCZ Resolution: 1.32→47.09 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.023 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.042 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.77 Å2 / Biso mean: 15.039 Å2 / Biso min: 8.17 Å2
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Refinement step | Cycle: final / Resolution: 1.32→47.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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