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- PDB-7wkl: Crystal structure of dihydroxybenzoate decarboxylase mutant F296Y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wkl | ||||||
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Title | Crystal structure of dihydroxybenzoate decarboxylase mutant F296Y from Aspergillus oryzae in complex with catechol | ||||||
![]() | Amidohydrolase 2 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fan, Y. / Xue, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase Authors: Fan, Y. / Wu, S. / Shi, J. / Li, X. / Yang, Y. / Feng, Y. / Xue, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 391.9 KB | Display | ![]() |
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PDB format | ![]() | 255.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
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Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 63.3 KB | Display | |
Data in CIF | ![]() | 97.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wkmC ![]() 7wmbC ![]() 2dvuS 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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Unit cell |
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Components
#1: Protein | Mass: 39060.004 Da / Num. of mol.: 4 / Mutation: F296Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CAQ / #4: Chemical | ChemComp-SO4 / #5: 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: 48.2 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M Sodium Chloride, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: May 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→30 Å / Num. obs: 118580 / % possible obs: 97.44 % / Redundancy: 11.5 % / Biso Wilson estimate: 19.49 Å2 / Rmerge(I) obs: 0.1774 / Rrim(I) all: 0.1855 / Net I/σ(I): 9.78 |
Reflection shell | Resolution: 1.87→1.94 Å / Rmerge(I) obs: 0.5524 / Mean I/σ(I) obs: 4.75 / Num. unique obs: 11301 / Rrim(I) all: 0.5766 / % possible all: 94.03 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DVU Resolution: 1.88→26.47 Å / SU ML: 0.1494 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.5844 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→26.47 Å
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Refine LS restraints |
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LS refinement shell |
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