+
Open data
-
Basic information
Entry | Database: PDB / ID: 5fax | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of subtilase SubHal from Bacillus halmapalus | |||||||||
![]() | Subtilase SubHal from Bacillus halmapalus | |||||||||
![]() | HYDROLASE / Protease / Subtilase / Calcium binding | |||||||||
Function / homology | ![]() 3.4.21.14 / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dohnalek, J. / Brzozowski, A.M. / Svendsen, A. / Wilson, K.S. | |||||||||
![]() | ![]() Journal: Book / Year: 2016 Title: Stabilization of Enzymes by Metal Binding: Structures of Two Alkalophilic Bacillus Subtilases and Analysis of the Second Metal-Binding Site of the Subtilase Family Authors: Dohnalek, J. / McAuley, K.E. / Brzozowski, A.M. / Oestergaard, P.R. / Svendsen, A. / Wilson, K.S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 187 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 145.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 455 KB | Display | |
Data in XML | ![]() | 39.3 KB | Display | |
Data in CIF | ![]() | 58.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fbzSC ![]() 5ffnC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45356.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal asparagine is naturally modified to N-carboxyasparagine. There is no associated Uniprot entry, however the sequence is available in patent WO 2004083362 Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.8 % / Description: Elongated plates |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein concentration 24 mg ml-1 in 50 mM sodium cacodylate buffer, pH 6.5, 2 mM CaCl2 and 100 mM NaCl. The enzyme was crystallised by hanging drop vapour diffusion in drops containing 1 ...Details: Protein concentration 24 mg ml-1 in 50 mM sodium cacodylate buffer, pH 6.5, 2 mM CaCl2 and 100 mM NaCl. The enzyme was crystallised by hanging drop vapour diffusion in drops containing 1 microliter of protein and 1 microliter of reservoir solution over 0.5 ml of reservoir: Hampton Screen 2 no. 23 (10% dioxane, 0.1 M 2-(N-Morpholino)-ethanesulphonic acid (MES) buffer, pH 6.5, 1.6 M ammonium sulphate). Clusters of elongated plates appeared after several days. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 41891 / Num. obs: 41891 / % possible obs: 74 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.4 / % possible all: 49.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Complex of SubHal with CI2A inhibitor, PDB ID 5FBZ Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.888 / SU B: 3.193 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.77 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|