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- PDB-8ywo: Crystal structure of L-azetidine-2-carboxylate hydrolase soaked i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ywo | ||||||
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Title | Crystal structure of L-azetidine-2-carboxylate hydrolase soaked in (S)-azetidine-2-carboxylic acid | ||||||
![]() | (S)-2-haloacid dehalogenase | ||||||
![]() | HYDROLASE / azetidine-2-carboxylate / dehalogenase / alpha/beta hydrolase | ||||||
Function / homology | (S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity / L-2-Haloacid dehalogenase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / (2S)-azetidine-2-carboxylic acid / (S)-2-haloacid dehalogenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Toyoda, M. / Mizutani, K. / Mikami, B. / Wackett, L.P. / Esaki, N. / Kurihara, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Research for the crystal structure of L-azetidine-2-carboxylate hydrolase Authors: Toyoda, M. / Jitsumori, K. / Mikami, B. / Mizutani, K. / Esaki, N. / Wackett, L.P. / Kurihara, 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 | ![]() | 153.1 KB | Display | ![]() |
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PDB format | ![]() | 100 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 728 KB | Display | ![]() |
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Full document | ![]() | 728.9 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8yvwC ![]() 3smvS 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: 27146.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-02A / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Precipitant: 20% PEG 3350, 0.15 M Magnesium acetate, 0.1 M imidazole/HCl buffer; Soaking: the precipitant above with 50 mM L-azetidine-2-carboxylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→40.43 Å / Num. obs: 32195 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.53 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.05 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.98 / Num. unique obs: 4744 / CC1/2: 0.869 / Rrim(I) all: 0.394 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SMV Resolution: 1.58→25.52 Å / SU ML: 0.1686 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9539 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→25.52 Å
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Refine LS restraints |
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LS refinement shell |
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