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Yorodumi- PDB-6vcw: Crystal structure of Medicago truncatula S-adenosylmethionine Syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vcw | ||||||
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Title | Crystal structure of Medicago truncatula S-adenosylmethionine Synthase 3A (MtMAT3A) | ||||||
Components | S-adenosylmethionine synthase | ||||||
Keywords | TRANSFERASE / methionine adenosyltransferase / SAM synthase | ||||||
Function / homology | Function and homology information methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 6vcw.cif.gz | 346.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vcw.ent.gz | 279.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vcw_validation.pdf.gz | 263.6 KB | Display | wwPDB validaton report |
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Full document | 6vcw_full_validation.pdf.gz | 263.6 KB | Display | |
Data in XML | 6vcw_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 6vcw_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/6vcw ftp://data.pdbj.org/pub/pdb/validation_reports/vc/6vcw | HTTPS FTP |
-Related structure data
Related structure data | 6vcxC 6vcyC 6vczC 6vd0C 6vd1C 6vd2C 5a1iS 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
#1: Protein | Mass: 42984.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Tissue: leaves / Gene: 11432371, MTR_7g102120, MtrunA17_Chr7g0264651 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7L3W1, methionine adenosyltransferase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | 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: 2.06 Å3/Da / Density % sol: 40.28 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.01 M CoCl2, 0.2 M MgCl2, 0.1 M Bis-Tris propane at pH 8.0, 6.25% PEG 3350, 6.25% PEG 4000, 6.25% PEG 2000, 6.25% mmPEG 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2017 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.99 Å / Num. obs: 130457 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 4.79 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.48 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 4.67 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 19394 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5a1i Resolution: 1.4→48.99 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.49 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053 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: 101.86 Å2 / Biso mean: 18.852 Å2 / Biso min: 8.51 Å2
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Refinement step | Cycle: final / Resolution: 1.4→48.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.433 Å / Rfactor Rfree error: 0
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