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Open data
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Basic information
Entry | Database: PDB / ID: 8jik | ||||||
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Title | Alanine decarboxylase | ||||||
![]() | Serine decarboxylase | ||||||
![]() | LYASE / PLP / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | ![]() carbon-carbon lyase activity / : / carboxylic acid metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gong, W. / Wang, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of alanine decarboxylase Authors: Gong, W. / Wang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.4 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.8 KB | Display | ![]() |
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Full document | ![]() | 464.1 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jijC 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, 1 molecules A
#1: Protein | Mass: 47725.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 64 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NEH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NEH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLP / |
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#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-NEH / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.8 M Sodium acetate trihydrate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 24010 / % possible obs: 99.6 % / Redundancy: 13 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.562 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 45.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→17.62 Å
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Refine LS restraints |
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