[English] 日本語
Yorodumi- PDB-1g6s: STRUCTURE OF EPSP SYNTHASE LIGANDED WITH SHIKIMATE-3-PHOSPHATE AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g6s | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF EPSP SYNTHASE LIGANDED WITH SHIKIMATE-3-PHOSPHATE AND GLYPHOSATE | ||||||
Components | EPSP SYNTHASE | ||||||
Keywords | TRANSFERASE / two-domain structure / 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: 1.5 Å | ||||||
Authors | Schonbrunn, E. / Eschenburg, S. / Shuttleworth, W. / Schloss, J.V. / Amrhein, N. / Evans, J.N.S. / Kabsch, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Interaction of the herbicide glyphosate with its target enzyme 5-enolpyruvylshikimate 3-phosphate synthase in atomic detail. Authors: Schonbrunn, E. / Eschenburg, S. / Shuttleworth, W.A. / Schloss, J.V. / Amrhein, N. / Evans, J.N. / Kabsch, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1g6s.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1g6s.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g6s_validation.pdf.gz | 826.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1g6s_full_validation.pdf.gz | 827 KB | Display | |
Data in XML | 1g6s_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 1g6s_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g6s ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g6s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46141.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AROA / Production host: Escherichia coli (E. coli) References: UniProt: P0A6D3, 3-phosphoshikimate 1-carboxyvinyltransferase | ||
---|---|---|---|
#2: Chemical | ChemComp-S3P / | ||
#3: Chemical | ChemComp-GPJ / | ||
#4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.63 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: pH 7, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 2, 2000 / Details: osmic mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 67479 / Num. obs: 67479 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 6.5 / Num. unique all: 5803 / % possible all: 89.2 |
Reflection | *PLUS Num. measured all: 201724 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 89.2 % / Num. unique obs: 6509 / Num. measured obs: 15899 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2789644.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.95 Å2 / ksol: 0.394 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 2.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.199 / % reflection Rfree: 2.8 % / Rfactor Rwork: 0.166 |