+Open data
-Basic information
Entry | Database: PDB / ID: 1jx0 | ||||||
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Title | Chalcone Isomerase--Y106F mutant | ||||||
Components | CHALCONE--FLAVONONE ISOMERASE 1 | ||||||
Keywords | ISOMERASE / monomer / unique fold | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Jez, J.M. / Bowman, M.E. / Noel, J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Role of Hydrogen Bonds in the Reaction Mechanism of Chalcone Isomerase Authors: Jez, J.M. / Bowman, M.E. / Noel, J.P. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: Structure and Mechanism of the Evolutionarily Unique Plant Enzyme Chalcone Isomerase Authors: Jez, J.M. / Bowman, M.E. / Dixon, R.A. / 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 | 1jx0.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jx0.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jx0 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jx0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23835.234 Da / Num. of mol.: 2 / Mutation: Y106F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Plasmid: pHIS8 (modified pET28b) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28012, chalcone isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-DFV / | #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: 4.27 Å3/Da / Density % sol: 71.18 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: glycerol, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 / Wavelength: 1.008 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2001 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→58.16 Å / Num. all: 19709 / Num. obs: 19709 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 56.2 Å2 / Rsym value: 0.064 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.85→2.98 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2456 / Rsym value: 0.516 / % possible all: 88.3 |
Reflection | *PLUS Highest resolution: 2.85 Å / Lowest resolution: 58 Å / Num. obs: 19000 / Num. measured all: 261225 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 96.1 % / Rmerge(I) obs: 0.516 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: wild-type chalcone isomerase with alanine at position 106 Resolution: 2.85→10 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 0.311596 Å2 / ksol: 54.0715 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.85 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→10 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 58 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.263 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.012 |