+Open data
-Basic information
Entry | Database: PDB / ID: 1c1m | ||||||
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Title | PORCINE ELASTASE UNDER XENON PRESSURE (8 BAR) | ||||||
Components | PROTEIN (PORCINE ELASTASE) | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / PANCREAS ELASTASE / XENON | ||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Prange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R. | ||||||
Citation | Journal: Proteins / Year: 1998 Title: Exploring hydrophobic sites in proteins with xenon or krypton. Authors: Prange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R. #1: Journal: J.Synchrotron Radiat. / Year: 1997 Title: Protein Crystallography at Ultra-Short Wavelengths: Feasability Study of Anomalous-Dispersion Experiments at the Xenon K-Edge Authors: Schiltz, M. / Kvick, A. / Svensson, O. / Shepard, W. / De La Fortelle, E. / Prange, T. / Kahn, R. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: High-Pressure Krypton Gas and Statistical Heavy Atom Refinement: A Successful Combination of Tools for Macromolecular Structure Determination Authors: Schiltz, M. / Shepard, W. / Fourme, R. / Prange, T. / De La Fortelle, E. / Bricogne, G. #3: Journal: Structure / Year: 1995 Title: The Active Site of Serine Proteinases as a Specific Binding Cavity for Xenon Authors: Schiltz, M. / Fourme, R. / Prange, T. #4: Journal: J.Appl.Crystallogr. / Year: 1994 Title: On the Preparation and X-Ray Data Collection of Isomorphous Xenon Derivatives Authors: Schiltz, M. / Prange, T. / Fourme, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c1m.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c1m.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/1c1m ftp://data.pdbj.org/pub/pdb/validation_reports/c1/1c1m | HTTPS FTP |
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-Related 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: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-XE / |
#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: 2.22 Å3/Da / Density % sol: 44.57 % | ||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 1.4 MG ENZYME IN 0.1 ML ACETATE BUFFER (0.05M) PLUS 0.0001 ML PRECIPITATING AGENT (SODIUM SULPHATE 1M), pH 5.50 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5 / Method: unknown / Details: Shotton, D.M., (1968) J.Mol.Biol., 32, 155. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.962 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.962 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→17.7 Å / Num. obs: 44217 / % possible obs: 93.9 % / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.146 / % possible all: 64 |
-Processing
Software |
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Refinement | Resolution: 2.2→17.7 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER Details: REFINED WITH A COMBINATION OF SHELXL AND WARP AUTOMATIC PROCEDURE FOR LOCALIZING AND ANALYSING THE WATER MOLECULES.
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Refinement step | Cycle: LAST / Resolution: 2.2→17.7 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.183 / Rfactor Rwork: 0.162 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |