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- PDB-7xwv: Feruloyl-CoA hydratase/lyase complexed with Vanillin and Coenzyme A -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xwv | ||||||
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Title | Feruloyl-CoA hydratase/lyase complexed with Vanillin and Coenzyme A | ||||||
![]() | Feruloyl-CoA hydratase/lyase | ||||||
![]() | LYASE / Feruloyl-CoA hydratase/lyase | ||||||
Function / homology | isoprenoid catabolic process / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / lyase activity / COENZYME A / IMIDAZOLE / 4-hydroxy-3-methoxybenzaldehyde / Feruloyl-CoA hydratase/lyase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seok, J. / Kim, K.-J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Production of various phenolic aldehyde compounds using the 4CL-FCHL biosynthesis platform. Authors: Seok, J. / Seo, H. / Hong, J. / Kim, K.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.4 KB | Display | ![]() |
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PDB format | ![]() | 90.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xwcC ![]() 7xwtC ![]() 2j5iS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33613.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 166 molecules ![](data/chem/img/V55.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-IMD / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.45 % / Mosaicity: 0.812 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium phosphate dibasic, Imidazole/Hydrochloric acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.81→50 Å / Num. obs: 71335 / % possible obs: 96.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.033 / Rrim(I) all: 0.101 / Χ2: 4.684 / Net I/σ(I): 16.7 / Num. measured all: 458140 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2j5i Resolution: 1.81→30.65 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.888 / SU B: 3.071 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.18 Å2 / Biso mean: 22.511 Å2 / Biso min: 10.55 Å2
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Refinement step | Cycle: final / Resolution: 1.81→30.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.815→1.862 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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