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Yorodumi- PDB-6vcy: Crystal structure of Arabidopsis thaliana S-adenosylmethionine Sy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vcy | ||||||
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Title | Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 1 (AtMAT1) in complex with 5'-methylthioadenosine | ||||||
Components | S-adenosylmethionine synthase 1 | ||||||
Keywords | TRANSFERASE / methionine adenosyltransferase / SAM synthase | ||||||
Function / homology | Function and homology information ethylene biosynthetic process / plant-type cell wall / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / extracellular region / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 | 6vcy.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vcy.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vcy_validation.pdf.gz | 351.8 KB | Display | wwPDB validaton report |
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Full document | 6vcy_full_validation.pdf.gz | 351.7 KB | Display | |
Data in XML | 6vcy_validation.xml.gz | 1.7 KB | Display | |
Data in CIF | 6vcy_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/6vcy ftp://data.pdbj.org/pub/pdb/validation_reports/vc/6vcy | HTTPS FTP |
-Related structure data
Related structure data | 6vcwC 6vcxSC 6vczC 6vd0C 6vd1C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43487.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: leaves / Gene: SAM1, At1g02500, T14P4.17, T14P4_22 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23686, methionine adenosyltransferase |
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-Non-polymers , 6 types, 365 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-MTA / | #6: Chemical | ChemComp-CL / #7: 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: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.8 M (NH4)2SO4, 0.08 M Bis-Tris |
-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: Apr 21, 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: 1.82→49.25 Å / Num. obs: 37699 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.53 |
Reflection shell | Resolution: 1.82→1.93 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 5980 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VCX Resolution: 1.82→49.25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.289 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.118 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 103.17 Å2 / Biso mean: 29.249 Å2 / Biso min: 17.72 Å2
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Refinement step | Cycle: final / Resolution: 1.82→49.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.822→1.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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