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Yorodumi- PDB-1t9a: Crystal structure of yeast acetohydroxyacid synthase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t9a | ||||||
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Title | Crystal structure of yeast acetohydroxyacid synthase in complex with a sulfonylurea herbicide, tribenuron methyl | ||||||
Components | Acetolactate synthase, mitochondrial | ||||||
Keywords | TRANSFERASE / acetohydroxyacid synthase / acetolactate synthase / herbicide / sulfonylurea / thiamin diphosphate / FAD / inhibitor / tribenuron methyl | ||||||
Function / homology | Function and homology information acetolactate synthase complex / acetolactate synthase / branched-chain amino acid biosynthetic process / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | McCourt, J.A. / Pang, S.S. / Guddat, L.W. / Duggleby, R.G. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Elucidating the specificity of binding of sulfonylurea herbicides to acetohydroxyacid synthase. Authors: McCourt, J.A. / Pang, S.S. / 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 | 1t9a.cif.gz | 272.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t9a.ent.gz | 212.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t9a_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1t9a_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1t9a_validation.xml.gz | 58.1 KB | Display | |
Data in CIF | 1t9a_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/1t9a ftp://data.pdbj.org/pub/pdb/validation_reports/t9/1t9a | HTTPS FTP |
-Related structure data
Related structure data | 1t9bC 1t9cC 1t9dC 1n0hS S: Starting model for refinement C: citing same article (ref.) |
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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 asymmetric unit contains the minimum biological unit required for activity, a dimer. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 73597.656 Da / Num. of mol.: 2 / Fragment: Catalytic Subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ILV2, SMR1, YMR108W, YM9718.07 / Plasmid: pET30(c) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07342, acetolactate synthase |
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-Non-polymers , 8 types, 925 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-YF3 / | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-YF4 / | #9: Water | ChemComp-HOH / | |
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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: 3.53 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: potassium phosphate, thiamin diphosphate, FAD, magnesium chloride, DTT, tribenuron methyl, Tris-HCl, Lithium sulfate, sodium potassium tartrate, pH 7.0, 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-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2002 / Details: mirrors |
Radiation | Monochromator: GE (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→99 Å / Num. obs: 67083 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.72 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.58→2.68 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.95 / Num. unique all: 5303 / % possible all: 78.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N0H Resolution: 2.59→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: 51.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.59→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.69 Å
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