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Open data
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Basic information
Entry | Database: PDB / ID: 5ysr | ||||||
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Title | Ethanolamine ammonia-lyase, AdoCbl/2-amino-1-propanol | ||||||
![]() | (Ethanolamine ammonia-lyase ...) x 2 | ||||||
![]() | LYASE / Adenosylcobalamin / Radical enzyme | ||||||
Function / homology | ![]() ethanolamine ammonia-lyase / ethanolamine ammonia-lyase activity / ethanolamine ammonia-lyase complex / ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / cobalamin binding / amino acid metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shibata, N. | ||||||
![]() | ![]() Title: Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis. Authors: Shibata, N. / Sueyoshi, Y. / Higuchi, Y. / Toraya, 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 | ![]() | 584.9 KB | Display | ![]() |
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PDB format | ![]() | 479.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 61.8 KB | Display | |
Data in CIF | ![]() | 85.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yrtC ![]() 5yrvC ![]() 5yshC ![]() 5ysnC ![]() 3abrS 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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1 | ![]()
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Unit cell |
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Components
-Ethanolamine ammonia-lyase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 49447.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 31819.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 659 molecules ![](data/chem/img/5AD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% (w/v) PEG 6000, 0.1M ammonium chloride, 0.05M Tris pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.75 |
Reflection | Resolution: 2.05→48 Å / Num. obs: 161685 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.121 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 11915 / CC1/2: 0.503 / Rrim(I) all: 0.764 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ABR Resolution: 2.05→48 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.53 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→48 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 94.56 Å / Origin y: -98.8337 Å / Origin z: -26.8922 Å
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Refinement TLS group | Selection details: all |