+Open data
-Basic information
Entry | Database: PDB / ID: 1cgk | ||||||
---|---|---|---|---|---|---|---|
Title | CHALCONE SYNTHASE FROM ALFALFA COMPLEXED WITH NARINGENIN | ||||||
Components | PROTEIN (CHALCONE SYNTHASE) | ||||||
Keywords | TRANSFERASE / POLYKETIDE SYNTHASE / CHALCONE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information chalcone biosynthetic process / chalcone synthase activity / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.84 Å | ||||||
Authors | Ferrer, J.-L. / Jez, J. / Bowman, M.E. / Dixon, R. / Noel, J.P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Authors: Ferrer, J.L. / Jez, J.M. / Bowman, M.E. / Dixon, R.A. / Noel, J.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1cgk.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1cgk.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/1cgk ftp://data.pdbj.org/pub/pdb/validation_reports/cg/1cgk | HTTPS FTP |
---|
-Related structure data
Related structure data | 1bi5SC 1bq6C 1cgzC 1chwC 1cmlC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 42755.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH NARINGENIN / Source: (gene. exp.) Medicago sativa (alfalfa) / Tissue: 21 DAY OLD ROOT NODULE / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30074, chalcone synthase |
---|---|
#2: Chemical | ChemComp-NAR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: THE DROPLE CONSISTED ON 25 MGR/ML (FINAL CONCENTRATION) PROTEIN MIXED WITH THE RESERVOIR WHICH CONTAINED 2.4 M AMMONIUM SULFATE, 100 MM PIPES BUFFER (PH 6.5) , IN THE PRESENCE (UP TO 5 MM) ...Details: THE DROPLE CONSISTED ON 25 MGR/ML (FINAL CONCENTRATION) PROTEIN MIXED WITH THE RESERVOIR WHICH CONTAINED 2.4 M AMMONIUM SULFATE, 100 MM PIPES BUFFER (PH 6.5) , IN THE PRESENCE (UP TO 5 MM) OR ABSENCE OF DTT REDUCING AGENT. CRYSTALS WERE STABILIZED IN 40% (V/V) PEG400, 100 MM PIPES 16 MM NARINGENIN PRIOR TO FREEZING AT 105 K, pH 6.50 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Jun 1, 1998 |
Radiation | Monochromator: 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: 1.84→51.68 Å / Num. obs: 26948 / % possible obs: 86.6 % / Redundancy: 2.8 % / Rsym value: 0.041 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.84→1.89 Å / Redundancy: 0.1 % / Mean I/σ(I) obs: 7.5 / Rsym value: 0.011 / % possible all: 8.3 |
Reflection | *PLUS Highest resolution: 1.84 Å / Lowest resolution: 51.68 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS Redundancy: 0.1 % / Mean I/σ(I) obs: 7.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1BI5 Resolution: 1.84→84.5 Å / σ(F): 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→84.5 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.162 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |