+Open data
-Basic information
Entry | Database: PDB / ID: 1be8 | ||||||
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Title | TRANS-CINNAMOYL-SUBTILISIN IN WATER | ||||||
Components | SUBTILISIN CARLSBERG | ||||||
Keywords | SERINE PROTEASE / ORGANIC SOLVENT / ACYL-ENZYME | ||||||
Function / homology | Function and homology information subtilisin / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Schmitke, J.L. / Stern, L.J. / Klibanov, A.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Comparison of x-ray crystal structures of an acyl-enzyme intermediate of subtilisin Carlsberg formed in anhydrous acetonitrile and in water. Authors: Schmitke, J.L. / Stern, L.J. / Klibanov, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1be8.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1be8.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 1be8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1be8_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 1be8_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 1be8_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 1be8_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/1be8 ftp://data.pdbj.org/pub/pdb/validation_reports/be/1be8 | HTTPS FTP |
-Related structure data
Related structure data | 1be6C 1scaS 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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Unit cell |
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-Components
#1: Protein | Mass: 27306.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-TCA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.86 % | ||||||||||||||||||||
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Crystal grow | pH: 3 Details: PROTEIN WAS CRYSTALLIZED FROM 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 5.6; THEN CROSS-LINKED WITH 10% GLUTARALDEHYDE IN 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 7.5, WASHED WITH DISTILLED ...Details: PROTEIN WAS CRYSTALLIZED FROM 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 5.6; THEN CROSS-LINKED WITH 10% GLUTARALDEHYDE IN 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 7.5, WASHED WITH DISTILLED WATER, AND TRANSFERRED TO WATER AND N-TRANS-CINNAMOYL IMIDAZOLE WAS ADDED., pH 3.0 PH range: 5.6-7.5 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 13, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→14 Å / Num. obs: 10193 / % possible obs: 88.6 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.1 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.41 / % possible all: 72.3 |
Reflection | *PLUS Num. obs: 10663 / Num. measured all: 57568 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 72.3 % / Num. unique obs: 1089 / Rmerge(I) obs: 0.415 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SCA Resolution: 2.2→14 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 10193 / Rfactor obs: 0.184 / Rfactor Rfree: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.292 / Num. reflection Rwork: 1055 / Rfactor obs: 0.256 |