+Open data
-Basic information
Entry | Database: PDB / ID: 1c3l | ||||||
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Title | SUBTILISIN-CARLSBERG COMPLEXED WITH XENON (8 BAR) | ||||||
Components | SUBTILISIN-CARLSBERG | ||||||
Keywords | HYDROLASE / XENON / SERINE-PROTEINASE | ||||||
Function / homology | Function and homology information subtilisin / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.16 Å | ||||||
Authors | Prange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. | ||||||
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.Appl.Crystallogr. / Year: 1994 Title: On the Preparation and X-ray Data Collection of Isomorphous Xenon Derivatives Authors: Schiltz, M. / Prange, T. / Fourme, R. #2: Journal: Structure / Year: 1995 Title: The Catalytic Site of Serine-Proteinases as a Specific Binding Cavity for Xenon Authors: Schiltz, M. / Fourme, R. / Broutin, I. / Prange, T. #3: Journal: J.Mol.Biol. / Year: 1976 Title: The Structure of Subtilopeptidase 1. X-ray Crystallographic Data Authors: Petsko, G.A. / Tsernoglou, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c3l.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3l.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c3l_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 1c3l_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | 1c3l_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 1c3l_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3l ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3l | HTTPS FTP |
-Related structure data
Related structure data | 1c10C 1c1mC 1qtkC 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: 27279.176 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 | #3: Chemical | ChemComp-XE / | #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: 2.07 Å3/Da / Density % sol: 40.57 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 5.5 Details: protein: 15mg/ml in acetate buffer (0.05M) plus sodium azide (10-5M). Sodium formate as the crystallizing agent(4M). Crystals as elongated needles in two weeks., pH 5.50, MICRODIALYSIS, temperature 298K | ||||||||||||||||||||
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: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.961 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.961 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→15 Å / Num. all: 44356 / Num. obs: 40233 / % possible obs: 0.83 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.16→2.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.167 / Num. unique all: 1172 / % possible all: 65 |
-Processing
Software |
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Refinement | Starting model: 1SCA Resolution: 2.16→7 Å / Num. parameters: 8135 / Num. restraintsaints: 7863 / σ(F): 3 / σ(I): 4 / Stereochemistry target values: Engh & Huber / Details: 8135 parameters refined using 7863 restraints
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Refinement step | Cycle: LAST / Resolution: 2.16→7 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 3 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |