+Open data
-Basic information
Entry | Database: PDB / ID: 5fax | |||||||||
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Title | Structure of subtilase SubHal from Bacillus halmapalus | |||||||||
Components | Subtilase SubHal from Bacillus halmapalus | |||||||||
Keywords | HYDROLASE / Protease / Subtilase / Calcium binding | |||||||||
Function / homology | Function and homology information 3.4.21.14 / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus halmapalus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Dohnalek, J. / Brzozowski, A.M. / Svendsen, A. / Wilson, K.S. | |||||||||
Citation | Book title: Understanding enzymes; Function, Design, Engineering and Analysis 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fax.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fax.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fax_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 5fax_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 5fax_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 5fax_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/5fax ftp://data.pdbj.org/pub/pdb/validation_reports/fa/5fax | HTTPS FTP |
-Related structure data
Related structure data | 5fbzSC 5ffnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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.) Bacillus halmapalus (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A182DWC7*PLUS, 3.4.21.14 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.8 % / Description: Elongated plates |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
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
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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
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Refinement step | Cycle: 1 / Resolution: 2→30 Å
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Refine LS restraints |
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