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Yorodumi- PDB-7fag: Room temperature structure of elastase with high-strength agarose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fag | ||||||||||||
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Title | Room temperature structure of elastase with high-strength agarose hydrogel | ||||||||||||
Components | Chymotrypsin-like elastase family member 1 | ||||||||||||
Keywords | ISOMERASE / elastase / high-strength hydrogel-grown crystal / / room temperature structure serine protease / hydrolase | ||||||||||||
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: 1.3 Å | ||||||||||||
Authors | Sugiyama, S. / Kakinouchi, K. / Adachi, H. / Murata, M. / Mori, Y. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: To Be Published Title: Room temperature structure of elastase with high-strength agarose hydrogel Authors: Sugiyama, S. / Kakinouchi, K. / Adachi, H. / Murata, M. / Mori, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fag.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fag.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 7fag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/7fag ftp://data.pdbj.org/pub/pdb/validation_reports/fa/7fag | HTTPS FTP |
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-Related structure data
Related structure data | 5avdS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CELA1, ELA1 / Production host: Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-SO3 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Na acetate (pH8.5), 0.03M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 54930 / % possible obs: 98.2 % / Redundancy: 4.7 % / Rpim(I) all: 0.044 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.3→1.32 Å / Num. unique obs: 2663 / Rpim(I) all: 0.314 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AVD Resolution: 1.3→26.91 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.725 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.944 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→26.91 Å
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Refine LS restraints |
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