[English] 日本語
Yorodumi- PDB-6sel: Multicrystal structure of Thermolysin at room temperature using a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sel | ||||||
---|---|---|---|---|---|---|---|
Title | Multicrystal structure of Thermolysin at room temperature using a multilayer monochromator. | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / DMM / multilayer monochromator / multicrystal | ||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sandy, J. / Sanchez-Weatherby, J. / Mikolajek, H. | ||||||
Citation | Journal: Iucrj / Year: 2023 Title: Protein-to-structure pipeline for ambient-temperature crystallography at VMXi Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.G. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6sel.cif.gz | 160.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6sel.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/6sel ftp://data.pdbj.org/pub/pdb/validation_reports/se/6sel | HTTPS FTP |
---|
-Related structure data
Related structure data | 6rvoC 6rzpC 6svaC 5a3yS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
---|
-Non-polymers , 5 types, 217 molecules
#2: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#3: Chemical | ChemComp-ILE / | ||
#4: Chemical | ChemComp-LYS / | ||
#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Protein dissolved in 50 mM MES pH 6.0, 45% (v/v) DMSO to a concentration of 100 mg/ ml. Equal amounts of the protein solution and a solution containing 50 mM MES pH 6.0, 1.0 M NaCl, 45% (v/v) ...Details: Protein dissolved in 50 mM MES pH 6.0, 45% (v/v) DMSO to a concentration of 100 mg/ ml. Equal amounts of the protein solution and a solution containing 50 mM MES pH 6.0, 1.0 M NaCl, 45% (v/v) DMSO were mixed and equilibrated over a well containing 35% (v/v) saturated solution of ammonium sulphate. |
-Data collection
Diffraction | Mean temperature: 293 K Ambient temp details: in situ experiment at room temperature Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Feb 13, 2019 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DMM (Double multilayer monochromator) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Biso Wilson estimate: 24.18 Å2 / Entry-ID: 6SEL
| ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A3Y Resolution: 2.2→81.02 Å / SU ML: 0.1677 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5475 Details: Data collected on three crystals were merged and reprocessed resulting in slightly better statistics (possibly due to different parameters used in processing). These merged data were used ...Details: Data collected on three crystals were merged and reprocessed resulting in slightly better statistics (possibly due to different parameters used in processing). These merged data were used for molecular replacement and were then refined.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→81.02 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|