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Yorodumi- PDB-7stq: Crystal structure of arabidopsis thaliana acetohydroxyacid syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7stq | ||||||
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Title | Crystal structure of arabidopsis thaliana acetohydroxyacid synthase W574L mutant in complex with chlorimuron-ethyl | ||||||
Components | Acetolactate synthase, chloroplastic | ||||||
Keywords | LIGASE / Herbicide / Resistance / AHAS / ALS | ||||||
Function / homology | Function and homology information acetolactate synthase activity / acetolactate synthase / valine biosynthetic process / isoleucine biosynthetic process / response to herbicide / thiamine pyrophosphate binding / chloroplast stroma / chloroplast / flavin adenine dinucleotide binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Guddat, L.W. / Cheng, Y. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of resistance to herbicides that target acetohydroxyacid synthase. Authors: Lonhienne, T. / Cheng, Y. / Garcia, M.D. / Hu, S.H. / Low, Y.S. / Schenk, G. / Williams, C.M. / 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 | 7stq.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7stq.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 7stq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/7stq ftp://data.pdbj.org/pub/pdb/validation_reports/st/7stq | HTTPS FTP |
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-Related structure data
Related structure data | 7tzzC 7u1dC 7u1uC 7u25C 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: 64518.609 Da / Num. of mol.: 1 / Mutation: W574L 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 , 6 types, 7 molecules
#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-CIE / | #5: Chemical | ChemComp-TZD / | #6: Chemical | ChemComp-NHE / | #7: Chemical | ChemComp-SO4 / | |
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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: 6.67 Å3/Da / Density % sol: 81.55 % / 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: 0.97 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→48.13 Å / Num. obs: 26470 / % possible obs: 99.6 % / Redundancy: 10.7 % / Biso Wilson estimate: 89.08 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.3→3.53 Å / Redundancy: 10.8 % / Num. unique obs: 4647 / Rpim(I) all: 0.197 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K2O Resolution: 3.3→48.13 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.77 / Stereochemistry target values: ML
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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 max: 173.07 Å2 / Biso mean: 83.6703 Å2 / Biso min: 40.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→48.13 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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