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- PDB-7bur: Chalcone synthase from Glycine max (L.) Merr (soybean) complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bur | |||||||||
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Title | Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin | |||||||||
![]() | Chalcone synthase 1 | |||||||||
![]() | TRANSFERASE / Isoflavonoid / Flavonoid / Soybean / PLANT PROTEIN | |||||||||
Function / homology | ![]() : / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Imaizumi, R. / Mameda, R. / Takeshita, K. / Waki, T. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. ...Imaizumi, R. / Mameda, R. / Takeshita, K. / Waki, T. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. / Yamashita, S. / Nakayama, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean. Authors: Imaizumi, R. / Mameda, R. / Takeshita, K. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. / Nakayama, T. / Yamashita, S. / Waki, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.9 KB | Display | ![]() |
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PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481 KB | Display | ![]() |
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Full document | ![]() | 485.2 KB | Display | |
Data in XML | ![]() | 37.7 KB | Display | |
Data in CIF | ![]() | 56.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7busC ![]() 6dxaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44648.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CIT / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate (pH 5.6). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→47.73 Å / Num. obs: 1023907 / % possible obs: 100 % / Redundancy: 13.35 % / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rrim(I) all: 0.188 / Net I/σ(I): 15.76 |
Reflection shell | Resolution: 1.82→1.93 Å / Redundancy: 12.72 % / Rmerge(I) obs: 1.868 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 12199 / CC1/2: 0.705 / Rrim(I) all: 1.946 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6DXA Resolution: 1.82→47.73 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.826 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.11 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.319 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→47.73 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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