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Yorodumi- PDB-1m4n: CRYSTAL STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH [2-(AMINO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m4n | ||||||
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Title | CRYSTAL STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH [2-(AMINO-OXY)ETHYL](5'-DEOXYADENOSIN-5'-YL)(METHYL)SULFONIUM | ||||||
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 / fruit ripening / 1-aminocyclopropane-1-carboxylate synthase activity / ethylene biosynthetic process / transaminase activity / pyridoxal phosphate binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Malus x domestica (apple) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Capitani, G. / Eliot, A.C. / Gut, H. / Khomutov, R.M. / Kirsch, J.F. / Grutter, M.G. | ||||||
Citation | Journal: BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS / Year: 2003 Title: Structure of 1-aminocyclopropane-1-carboxylate synthase in complex with an amino-oxy analogue of the substrate: implications for substrate binding. Authors: Capitani, G. / Eliot, A.C. / Gut, H. / Khomutov, R.M. / Kirsch, J.F. / Grutter, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m4n.cif.gz | 105.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m4n.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/1m4n ftp://data.pdbj.org/pub/pdb/validation_reports/m4/1m4n | 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: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P37821, 1-aminocyclopropane-1-carboxylate synthase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-AAD / ( |
#4: Chemical | ChemComp-MES / |
#5: 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: 2.1 Å3/Da / Density % sol: 41.53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 30, 2000 / Details: double focussing mirrors (Prophysics) |
Radiation | Monochromator: MIRRORS (PROPHYSICS) + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→23.77 Å / Num. obs: 26106 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.01→2.06 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / Num. unique all: 1185 / % possible all: 66.5 |
Reflection | *PLUS Lowest resolution: 24 Å |
Reflection shell | *PLUS % possible obs: 66.5 % / Rmerge(I) obs: 0.29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B8G Resolution: 2.01→23.77 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: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→23.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.08 Å
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Refinement | *PLUS Lowest resolution: 24 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.06 Å |