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- PDB-7xrn: Ethanolamine ammonia-lyase complexed with AdoMeCbl in the presenc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xrn | ||||||
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Title | Ethanolamine ammonia-lyase complexed with AdoMeCbl in the presence of substrate | ||||||
![]() | (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. / Toraya, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase. Authors: Shibata, N. / Higuchi, Y. / Krautler, B. / 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 | ![]() | 571.6 KB | Display | ![]() |
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PDB format | ![]() | 472.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xrkC ![]() 7xrlC ![]() 7xrmC ![]() 3abrS 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
-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: 28769.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 781 molecules ![](data/chem/img/FWK.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/B12.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: 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: 4.15 Å3/Da / Density % sol: 70.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% (w/v) PEG 6000, 0.1 M Ammonium chloride, and 0.05 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→49 Å / Num. obs: 156031 / % possible obs: 99.9 % / Redundancy: 6.82 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.77 |
Reflection shell | Resolution: 2.07→2.12 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 156031 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ABR Resolution: 2.07→48.16 Å / Cross valid method: FREE R-VALUE / σ(F): 60.09 / Phase error: 29.243 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: 35.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→48.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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