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Yorodumi- PDB-1mi4: Glyphosate insensitive G96A mutant EPSP synthase liganded with sh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mi4 | ||||||
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Title | Glyphosate insensitive G96A mutant EPSP synthase liganded with shikimate-3-phosphate | ||||||
Components | 5-enolpyruvylshikimate-3-phosphate synthase | ||||||
Keywords | TRANSFERASE / inside-out alpha-beta barrel | ||||||
Function / homology | Function and homology information 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Eschenburg, S. / Healy, M.L. / Priestman, M.A. / Lushington, G.H. / Schonbrunn, E. | ||||||
Citation | Journal: PLANTA / Year: 2002 Title: How the mutation glycine96 to alanine confers glyphosate insensitivity to 5-enolpyruvyl shikimate-3-phosphate synthase from Escherichia coli. Authors: Eschenburg, S. / Healy, M.L. / Priestman, M.A. / Lushington, G.H. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mi4.cif.gz | 106.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mi4.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/1mi4 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/1mi4 | HTTPS FTP |
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-Related structure data
Related structure data | 1g6tS S: Starting model for refinement |
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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: 46155.637 Da / Num. of mol.: 1 / Mutation: G96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aroA / Plasmid: pET24D / Production host: Escherichia coli (E. coli) References: UniProt: P0A6D3, 3-phosphoshikimate 1-carboxyvinyltransferase | ||
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#2: Chemical | ChemComp-S3P / | ||
#3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.36 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / pH: 7.8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2001 / Details: confocal mirrors |
Radiation | Monochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. all: 47038 / Num. obs: 47038 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.7→1.75 Å / Rmerge(I) obs: 0.346 / Num. unique all: 3815 / % possible all: 96 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 15 Å / Num. measured all: 199475 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 96 % / Num. unique obs: 3815 / Num. measured obs: 16125 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G6T Resolution: 1.7→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 2.5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |