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Yorodumi- PDB-1hi3: Eosinophil-derived Neurotoxin (EDN) - Adenosine 2'-5'-Diphosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hi3 | ||||||
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Title | Eosinophil-derived Neurotoxin (EDN) - Adenosine 2'-5'-Diphosphate Complex | ||||||
Components | EOSINOPHIL-DERIVED NEUROTOXIN | ||||||
Keywords | HYDROLASE / RNASE-2 / RNASE US / RIBONUCLEASE | ||||||
Function / homology | Function and homology information RNA catabolic process / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / innate immune response in mucosa / chemotaxis / azurophil granule lumen / defense response to virus / nucleic acid binding / lyase activity ...RNA catabolic process / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / innate immune response in mucosa / chemotaxis / azurophil granule lumen / defense response to virus / nucleic acid binding / lyase activity / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Leonidas, D.D. / Boix, E. / Prill, R. / Suzuki, M. / Turton, R. / Minson, K. / Swaminathan, G.J. / Youle, R.J. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Mapping the Ribonucleolytic Active Site of Eosinophil-Derived Neurotoxin (Edn): High Resolution Crystal Structures of Edn Complexes with Adenylic Nucleotide Inhibitors Authors: Leonidas, D.D. / Boix, E. / Prill, R. / Suzuki, M. / Turton, R. / Minson, K. / Swaminathan, G.J. / Youle, R.J. / Acharya, K.R. #1: Journal: J.Mol.Biol. / Year: 1996 Title: X-Ray Crystallographic Structure of Recombinant Eosinophil-Derived Neurotoxin at 1.83 A Resolution Authors: Mosimann, S.C. / Newton, D.L. / Youle, R.J. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hi3.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hi3.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 1hi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hi3_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 1hi3_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 1hi3_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1hi3_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/1hi3 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/1hi3 | HTTPS FTP |
-Related 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: 15611.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: EOSINOPHIL / Cellular location: SECRETORY GRANULES / Organelle: GRANULE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P10153, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-A2P / |
#3: 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: 1.34 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 1.5M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE PH 6.5, 5% ETHANOL | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 11471 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 14 / Rsym value: 0.161 / % possible all: 95.8 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 96.4 % / Num. measured all: 130116 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 90.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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