[English] 日本語
Yorodumi- PDB-8vsy: Bile salt hydrolase from Arthrobacter citreus with covalent inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vsy | ||||||
---|---|---|---|---|---|---|---|
Title | Bile salt hydrolase from Arthrobacter citreus with covalent inhibitor AAA-10 bound | ||||||
Components | Bile salt hydrolase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Inhibitor bound / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Chem-WSR Function and homology information | ||||||
Biological species | Arthrobacter citreus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Dhindwal, P. / Ruzzini, A. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: To Be Published Title: Bile salt hydrolase from Arthrobacter citreus with covalent inhibitor AAA-10 bound Authors: Dhindwal, P. / Ruzzini, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vsy.cif.gz | 160.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vsy.ent.gz | 123.6 KB | Display | PDB format |
PDBx/mmJSON format | 8vsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vsy_validation.pdf.gz | 945.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8vsy_full_validation.pdf.gz | 948.5 KB | Display | |
Data in XML | 8vsy_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 8vsy_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/8vsy ftp://data.pdbj.org/pub/pdb/validation_reports/vs/8vsy | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35322.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter citreus (bacteria) / Production host: Escherichia coli BL21 (bacteria) |
---|
-Non-polymers , 5 types, 782 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.14 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M HEPES, 21% PEG3350, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.41 Å / Num. obs: 77222 / % possible obs: 98.22 % / Redundancy: 6.9 % / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.6→1.657 Å / Num. unique obs: 7571 / CC1/2: 0.944 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.95 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.36 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→42.95 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|