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Yorodumi- PDB-1iay: CRYSTAL STRUCTURE OF ACC SYNTHASE COMPLEXED WITH COFACTOR PLP AND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iay | ||||||
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Title | CRYSTAL STRUCTURE OF ACC SYNTHASE COMPLEXED WITH COFACTOR PLP AND INHIBITOR AVG | ||||||
Components | 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2 | ||||||
Keywords | LYASE / protein-cofactor-inhibitor complex / V6-dependent enzyme | ||||||
Function / homology | Function and homology information 1-aminocyclopropane-1-carboxylate synthase / fruit ripening / 1-aminocyclopropane-1-carboxylate synthase activity / ethylene biosynthetic process / amino acid metabolic process / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Huai, Q. / Xia, Y. / Chen, Y. / Callahan, B. / Li, N. / Ke, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structures of 1-aminocyclopropane-1-carboxylate (ACC) synthase in complex with aminoethoxyvinylglycine and pyridoxal-5'-phosphate provide new insight into catalytic mechanisms Authors: Huai, Q. / Xia, Y. / Chen, Y. / Callahan, B. / Li, N. / Ke, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iay.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iay.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 1iay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iay_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 1iay_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 1iay_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1iay_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1iay ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1iay | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48294.113 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-438 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Plasmid: PET11D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P18485, 1-aminocyclopropane-1-carboxylate synthase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-AVG / |
#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: 2.42 Å3/Da / Density % sol: 49.12 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Na citrate, 18% PEG3350, 50 mM MgCl2, 10% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12C / Wavelength: 1 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD |
Radiation | 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: 13199 / Num. obs: 13199 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.7→2.9 Å / Rmerge(I) obs: 0.445 / % possible all: 76.2 |
Reflection | *PLUS Num. measured all: 62671 |
Reflection shell | *PLUS % possible obs: 76.2 % / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
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Displacement parameters | Biso mean: 30.1 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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