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Yorodumi- PDB-2fx4: Bovine trypsin bound by 4-piperidinebutyrate to make acylenzyme c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fx4 | ||||||
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Title | Bovine trypsin bound by 4-piperidinebutyrate to make acylenzyme complex | ||||||
Components | trypsin | ||||||
Keywords | HYDROLASE / serine protease / acylenzyme complex | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.65 Å | ||||||
Authors | Katz, B.A. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Structure-guided design of Peptide-based tryptase inhibitors. Authors: McGrath, M.E. / Sprengeler, P.A. / Hirschbein, B. / Somoza, J.R. / Lehoux, I. / Janc, J.W. / Gjerstad, E. / Graupe, M. / Estiarte, A. / Venkataramani, C. / Liu, Y. / Yee, R. / Ho, J.D. / ...Authors: McGrath, M.E. / Sprengeler, P.A. / Hirschbein, B. / Somoza, J.R. / Lehoux, I. / Janc, J.W. / Gjerstad, E. / Graupe, M. / Estiarte, A. / Venkataramani, C. / Liu, Y. / Yee, R. / Ho, J.D. / Green, M.J. / Lee, C.-S. / Liu, L. / Tai, V. / Spencer, J. / Sperandio, D. / Katz, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fx4.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fx4.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/2fx4 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/2fx4 | HTTPS FTP |
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-Related structure data
Related structure data | 2fpzC 2fs8C 2fs9C 2fwwC 2fx6C 2fxrC 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: 23324.287 Da / Num. of mol.: 1 / Fragment: cationic trypsin, residues 21-243 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-C1R / |
#4: 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: 3.02 Å3/Da / Density % sol: 59.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.2 Details: 25-35 mg/ml protein, 10 mM benzamidine, 0.9-1.2 M Magnesium sulfate, 25-50 mM Tris-HCl, 1.0 mM CaCl2, hanging/sitting drop, 4piperidinebutyrate, pH 8.20, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2004 / Details: Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→37.7 Å / Num. all: 34643 / Num. obs: 34643 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 1.65→1.74 Å / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 2 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.65→7 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.65→7 Å
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Refine LS restraints |
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