+Open data
-Basic information
Entry | Database: PDB / ID: 1s5s | ||||||
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Title | Porcine trypsin complexed with guanidine-3-propanol inhibitor | ||||||
Components | Trypsin | ||||||
Keywords | HYDROLASE / Serine protease | ||||||
Function / homology | Function and homology information trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Transue, T.R. / Krahn, J.M. / Gabel, S.A. / DeRose, E.F. / London, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: X-ray and NMR characterization of covalent complexes of trypsin, borate, and alcohols. Authors: Transue, T.R. / Krahn, J.M. / Gabel, S.A. / DeRose, E.F. / London, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s5s.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s5s.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s5s_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 1s5s_full_validation.pdf.gz | 436.3 KB | Display | |
Data in XML | 1s5s_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1s5s_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/1s5s ftp://data.pdbj.org/pub/pdb/validation_reports/s5/1s5s | HTTPS FTP |
-Related structure data
Related structure data | 1s6fC 1s6hC 1s81C 1s82C 1s83C 1s84C 1s85C 1aksS 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: 23493.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P00761, trypsin | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-PG3 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.19 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 8 Details: 1.8M MgSO4, 50mM HEPES, 5mM CaCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 2002 / Details: MSC/YALE DOUBLE FOCUSING MIRRORS |
Radiation | Monochromator: MSC/YALE DOUBLE FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. obs: 33968 / % possible obs: 88.7 % / Observed criterion σ(I): -3 / Redundancy: 7.467 % / Rsym value: 0.056 / Net I/σ(I): 25.0909 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.163 / Rsym value: 0.171 / % possible all: 73.5 |
Reflection | *PLUS Highest resolution: 1.4 Å / % possible obs: 89.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AKS Resolution: 1.4→43.78 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: AMBER98
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Displacement parameters | Biso mean: 14.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→43.78 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.4 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |