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Yorodumi- PDB-7pxy: Crystal structure of Arabidopsis thaliana 5-enol-pyruvyl-shikimat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pxy | ||||||
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Title | Crystal structure of Arabidopsis thaliana 5-enol-pyruvyl-shikimate-3-phosphate synthase (EPSPS) in open conformation | ||||||
Components | 3-phosphoshikimate 1-carboxyvinyltransferase, chloroplasticEPSP synthase | ||||||
Keywords | PLANT PROTEIN / glyphosate / herbicide design / EPSP synthase | ||||||
Function / homology | Function and homology information 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chloroplast stroma / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / chloroplast Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Ruszkowski, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2022 Title: Deciphering the structure of Arabidopsis thaliana 5- enol -pyruvyl-shikimate-3-phosphate synthase: An essential step toward the discovery of novel inhibitors to supersede glyphosate. Authors: Ruszkowski, M. / Forlani, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pxy.cif.gz | 241.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pxy.ent.gz | 159.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/7pxy ftp://data.pdbj.org/pub/pdb/validation_reports/px/7pxy | HTTPS FTP |
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-Related structure data
Related structure data | 3nvsS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 47872.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g45300, F4L23.19 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P05466, 3-phosphoshikimate 1-carboxyvinyltransferase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 75% of Index G12 (0.2 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350) + 10 mM glyphosate 2+2 drop Cryoprotection: Index G12+20% ethylene glycol; 0.5 ul ...Details: 75% of Index G12 (0.2 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350) + 10 mM glyphosate 2+2 drop Cryoprotection: Index G12+20% ethylene glycol; 0.5 ul of 200 mM glyphosate was added to 10 ul of cryo solution |
-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: Oct 20, 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: 1.4→80 Å / Num. obs: 92087 / % possible obs: 99.9 % / Redundancy: 18.5 % / Biso Wilson estimate: 22.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14710 / CC1/2: 0.784 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3nvs Resolution: 1.4→47.08 Å / SU ML: 0.1729 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5411 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Anisotropic refinement of ADPs,
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→47.08 Å
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Refine LS restraints |
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LS refinement shell |
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