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Yorodumi- PDB-1m7y: Crystal structure of apple ACC synthase in complex with L-aminoet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m7y | ||||||
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Title | Crystal structure of apple ACC synthase in complex with L-aminoethoxyvinylglycine | ||||||
Components | 1-aminocyclopropane-1-carboxylate synthase | ||||||
Keywords | LYASE / Fruit ripening / Ethylene biosynthesis / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH2 group of donors / 1-aminocyclopropane-1-carboxylate synthase / 1-aminocyclopropane-1-carboxylate synthase activity / fruit ripening / ethylene biosynthetic process / pyridoxal phosphate binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Malus x domestica (apple) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Capitani, G. / McCarthy, D. / Gut, H. / Gruetter, M.G. / Kirsch, J.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Apple 1-Aminocyclopropane-1-carboxylate Synthase in Complex with the Inhibitor L-Aminoethoxyvinylglycine Authors: Capitani, G. / McCarthy, D.L. / Gut, H. / Gruetter, M.G. / Kirsch, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m7y.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m7y.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 1m7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m7y ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m7y | HTTPS FTP |
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-Related structure data
Related structure data | 1b8gS 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 on special symmetry positions |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 49091.797 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-435 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Malus x domestica (apple) / Tissue: FRUIT CORTICAL / Plasmid: pET19bV435stopACS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS References: UniProt: P37821, 1-aminocyclopropane-1-carboxylate synthase |
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#2: Chemical | ChemComp-PPG / ( |
#3: Chemical | ChemComp-MRD / ( |
#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: 2.07 Å3/Da / Density % sol: 40.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.79955 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 2000 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.79955 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→15 Å / Num. obs: 50871 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.6→1.64 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2684 / % possible all: 76 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 15 Å / Num. obs: 50540 |
Reflection shell | *PLUS % possible obs: 76 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B8G Resolution: 1.6→14.924 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used bulk solvent correction (CNS 1.0)
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Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→14.924 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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