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Yorodumi- PDB-1yi0: Crystal structure of Arabidopsis thaliana Acetohydroxyacid syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yi0 | ||||||
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Title | Crystal structure of Arabidopsis thaliana Acetohydroxyacid synthase In Complex With A Sulfonylurea Herbicide, Sulfometuron methyl | ||||||
Components | Acetolactate synthase | ||||||
Keywords | TRANSFERASE / Acetohydroxyacid synthase / acetolactate synthase / herbicide / sulfonylurea / thiamin diphosphate / FAD / inhibitor / cysteine-s-dioxide / CHES / sulfometuron methyl | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.7 Å | ||||||
Authors | McCourt, J.A. / Pang, S.S. / King-Scott, J. / Guddat, L.W. / Duggleby, R.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase Authors: McCourt, J.A. / Pang, S.S. / King-Scott, J. / Guddat, L.W. / Duggleby, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yi0.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yi0.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/1yi0 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/1yi0 | HTTPS FTP |
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-Related structure data
Related structure data | 1ybhSC 1yhyC 1yhzC 1yi1C 1z8nC 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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2 |
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Unit cell |
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Details | The biological unit is a tetramer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64591.664 Da / Num. of mol.: 1 / Fragment: residues 86-667 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ILVB / Plasmid: pET30a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17597, acetolactate synthase |
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-Non-polymers , 6 types, 339 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-1SM / |
#4: Chemical | ChemComp-NHE / |
#5: Chemical | ChemComp-P22 / |
#6: Chemical | ChemComp-FAD / |
#7: 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: 6.6 Å3/Da / Density % sol: 80.6 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: Tris, FAD, DTT, ThDP, magnesium chloride, sulfometuron methyl, CHES, lithium sufate, potassium sodium tartrate , pH 9.0-9.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2003 / Details: mirrors |
Radiation | Monochromator: GE(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 45961 / Num. obs: 45961 / % possible obs: 95.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 4484 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1YBH Resolution: 2.7→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 59.682 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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LS refinement shell | Resolution: 2.7→2.8 Å
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