+Open data
-Basic information
Entry | Database: PDB / ID: 1lkb | ||||||
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Title | Porcine Pancreatic Elastase/Na-Complex | ||||||
Components | Elastase 1 | ||||||
Keywords | HYDROLASE / chymotrypsin-fold / beta-barrel / sodium binding / chloride binding / sulfate binding | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Weiss, M.S. / Panjikar, S. / Nowak, E. / Tucker, P.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Metal binding to porcine pancreatic elastase: calcium or not calcium. Authors: Weiss, M.S. / Panjikar, S. / Nowak, E. / Tucker, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lkb.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lkb.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 1lkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/1lkb ftp://data.pdbj.org/pub/pdb/validation_reports/lk/1lkb | HTTPS FTP |
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-Related structure data
Related structure data | 1lkaC 1qnjS C: citing same article (ref.) S: Starting model for refinement |
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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: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NA / | #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: 2.09 Å3/Da / Density % sol: 41.07 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: sodium acetate, sodium sulfate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.5 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→99 Å / Num. all: 24415 / Num. obs: 24415 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 56.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 18.6 / % possible all: 99 |
Reflection | *PLUS Redundancy: 19.12 % / Num. measured all: 466785 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1QNJ Resolution: 1.7→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints | Type: p_bond_d / Dev ideal: 0.01 | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 0 / Rfactor Rfree: 0.2034 / Rfactor Rwork: 0.1693 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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