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Yorodumi- PDB-1l1g: The Structure of Porcine Pancreatic Elastase Complexed with Xenon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l1g | ||||||
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Title | The Structure of Porcine Pancreatic Elastase Complexed with Xenon and Bromide, Cryoprotected with Glycerol | ||||||
Components | ELASTASE 1 | ||||||
Keywords | HYDROLASE / Xenon / Bromide / PPE | ||||||
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 / MAD / Resolution: 1.5 Å | ||||||
Authors | Panjikar, S. / Tucker, P.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Xenon derivatization of halide-soaked protein crystals. Authors: Panjikar, S. / 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 | 1l1g.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l1g.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1l1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/1l1g ftp://data.pdbj.org/pub/pdb/validation_reports/l1/1l1g | HTTPS FTP |
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-Related structure data
Related structure data | 1l0zC 1qnjS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: P00772, pancreatic elastase |
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-Non-polymers , 6 types, 225 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | ChemComp-NA / | ||||||
#4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-XE / | #6: Chemical | ChemComp-GOL / | #7: 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: 40.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10 mM sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Details: Shotton, D.M., (1968) J. Mol. Biol., 32, 155. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 29, 2001 |
Radiation | Protocol: SAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→35 Å / Num. all: 34589 / Num. obs: 34589 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.4 % / Biso Wilson estimate: 12.4 Å2 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. obs: 66284 / % possible obs: 99 % / Num. measured all: 1017166 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 1.22 Å / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1QNJ Resolution: 1.5→35 Å / Isotropic thermal model: Individual / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: HOH 1267 IS AN ALTERNATE CONFORMATION OF BR 267
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Refinement step | Cycle: LAST / Resolution: 1.5→35 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 35 Å / Rfactor all: 0.173 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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