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Yorodumi- PDB-8et5: Crystal structure of arabidopsis thaliana acetohydroxyacid syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8et5 | ||||||
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Title | Crystal structure of arabidopsis thaliana acetohydroxyacid synthase S653T mutant in complex with amidosulfuron | ||||||
Components | Acetolactate synthase, chloroplastic | ||||||
Keywords | TRANSFERASE / Herbicide / Resistance / AHAS / ALS / LIGASE | ||||||
Function / homology | Function and homology information acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma / amino acid biosynthetic process / chloroplast ...acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma / amino acid biosynthetic process / chloroplast / flavin adenine dinucleotide binding / magnesium ion binding / mitochondrion Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å | ||||||
Authors | Guddat, L.W. / Cheng, Y. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2023 Title: Crystal Structure of the Commercial Herbicide, Amidosulfuron, in Complex with Arabidopsis thaliana Acetohydroxyacid Synthase. Authors: Cheng, Y. / Lonhienne, T. / Garcia, M.D. / Williams, C.M. / Schenk, G. / Guddat, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8et5.cif.gz | 163.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8et5.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 8et5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8et5_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8et5_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8et5_validation.xml.gz | 24 KB | Display | |
Data in CIF | 8et5_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/8et5 ftp://data.pdbj.org/pub/pdb/validation_reports/et/8et5 | HTTPS FTP |
-Related structure data
Related structure data | 8et4C 5k2oS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64605.688 Da / Num. of mol.: 1 / Mutation: S653T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ALS, AHAS, CSR1, TZP5, At3g48560, T8P19.70 / Production host: Escherichia coli (E. coli) / References: UniProt: P17597, acetolactate synthase |
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-Non-polymers , 8 types, 13 molecules
#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-WRQ / | #5: Chemical | ChemComp-NHE / | #6: Chemical | ChemComp-AUJ / | #7: Chemical | ChemComp-TLA / | #8: Chemical | ChemComp-SO4 / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 6.77 Å3/Da / Density % sol: 81.83 % / Description: Yellow diamond shape |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.8 Details: CHES buffer, potassium sodium tartrate, sodium sulfate PH range: 9.4-9.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→48.28 Å / Num. obs: 37732 / % possible obs: 99.6 % / Redundancy: 14.6 % / Biso Wilson estimate: 66.74 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.046 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.94→3.07 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4382 / CC1/2: 0.835 / Rpim(I) all: 0.369 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K2O Resolution: 2.94→48.28 Å / SU ML: 0.3674 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8761 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 61.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→48.28 Å
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Refine LS restraints |
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LS refinement shell |
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