+Open data
-Basic information
Entry | Database: PDB / ID: 2ggd | ||||||
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Title | CP4 EPSP synthase Ala100Gly liganded with S3P and Glyphosate | ||||||
Components | 3-phosphoshikimate 1-carboxyvinyltransferase | ||||||
Keywords | TRANSFERASE / inside-out alpha/beta barrel / two domain structure | ||||||
Function / homology | Function and homology information shikimate kinase activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase activity / response to herbicide / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Agrobacterium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Schonbrunn, E. / Funke, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Molecular basis for the herbicide resistance of Roundup Ready crops. Authors: Funke, T. / Han, H. / Healy-Fried, M.L. / Fischer, M. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ggd.cif.gz | 106.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ggd.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ggd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ggd_validation.pdf.gz | 837.8 KB | Display | wwPDB validaton report |
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Full document | 2ggd_full_validation.pdf.gz | 839.2 KB | Display | |
Data in XML | 2ggd_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 2ggd_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/2ggd ftp://data.pdbj.org/pub/pdb/validation_reports/gg/2ggd | HTTPS FTP |
-Related structure data
Related structure data | 2gg4C 2gg6C 2ggaSC C: citing same article (ref.) 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: 47623.312 Da / Num. of mol.: 1 / Mutation: A100G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium sp. (bacteria) / Strain: CP4 / Gene: aroA / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9R4E4, 3-phosphoshikimate 1-carboxyvinyltransferase |
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#2: Chemical | ChemComp-S3P / |
#3: Chemical | ChemComp-GPJ / |
#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: 2.19 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: (NH4)2SO4/KCL/PEG400/HEPES-NA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 20, 2006 / Details: mirrors |
Radiation | Monochromator: rigaku 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: 44077 / Num. obs: 43324 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.078 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 6.8 / Num. unique all: 4254 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GGA Resolution: 1.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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