+Open data
-Basic information
Entry | Database: PDB / ID: 1fm8 | ||||||
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Title | CHALCONE ISOMERASE COMPLEXED WITH 5,4'-DIDEOXYFLAVANONE | ||||||
Components | CHALCONE-FLAVONONE ISOMERASE 1 | ||||||
Keywords | ISOMERASE / natural product biosynthesis / chalcone | ||||||
Function / homology | Function and homology information chalcone isomerase / chalcone isomerase activity / flavonoid biosynthetic process Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 2.3 Å | ||||||
Authors | Jez, J.M. / Noel, J.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Reaction mechanism of chalcone isomerase. pH dependence, diffusion control, and product binding differences. Authors: Jez, J.M. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fm8.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fm8.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/1fm8 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/1fm8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23851.236 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Plasmid: PET-28A(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P28012, chalcone isomerase #2: Chemical | #3: Chemical | ChemComp-DDC / | #4: 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: 4.98 Å3/Da / Density % sol: 75.12 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8-2.0 M ammonium sulfate, 25% glycerol, 0.05 M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0088 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0088 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→41 Å / Num. all: 658360 / Num. obs: 38121 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Redundancy: 17.3 % / Biso Wilson estimate: 43.2414 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1854 / % possible all: 99.1 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 38919 / % possible obs: 98 % / Num. measured all: 658360 |
Reflection shell | *PLUS % possible obs: 99.1 % |
-Processing
Software |
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Refinement | Method to determine structure: Difference Fourier Starting model: Chi apoenzyme Resolution: 2.3→41 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→41 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 41 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.238 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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