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Yorodumi- PDB-5avd: The 0.86 angstrom structure of elastase crystallized in high-stre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5avd | ||||||||||||
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Title | The 0.86 angstrom structure of elastase crystallized in high-strength agarose hydrogel | ||||||||||||
Components | Chymotrypsin-like elastase family member 1 | ||||||||||||
Keywords | ISOMERASE / elastase / high-strength agarose / hydrogel | ||||||||||||
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: 0.86 Å | ||||||||||||
Authors | Sugiyama, S. / Shimizu, N. / Maruyama, M. / Sazaki, G. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Growth of protein crystals in hydrogels prevents osmotic shock Authors: Sugiyama, S. / Maruyama, M. / Sazaki, G. / Hirose, M. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5avd.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5avd.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 5avd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/5avd ftp://data.pdbj.org/pub/pdb/validation_reports/av/5avd | HTTPS FTP |
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-Related structure data
Related structure data | 5avgC 5avhC 5avnC 1gvkS 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: 25928.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CELA1, ELA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00772, pancreatic elastase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE CONFLICT D92N IS BASED ON REFERENCE PUBMED IS 4578945 ACCORDING TO DATABASE P00772 (CELA1_PIG) | |
-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: 41.1 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5 / Details: 0.1 M Na acetate (pH 5.0), 0.03 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.86→50 Å / Num. obs: 174535 / % possible obs: 94.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 0.86→0.87 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.2 / % possible all: 77.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GVK Resolution: 0.86→45.85 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.34 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / 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: 10.282 Å2
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Refinement step | Cycle: LAST / Resolution: 0.86→45.85 Å
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Refine LS restraints |
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