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Yorodumi- PDB-2c01: Crystal Structures of Eosinophil-derived Neurotoxin in Complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c01 | ||||||
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Title | Crystal Structures of Eosinophil-derived Neurotoxin in Complex with the Inhibitors 5'-ATP, Ap3A, Ap4A and Ap5A | ||||||
Components | NONSECRETORY RIBONUCLEASE | ||||||
Keywords | HYDROLASE / ENDONUCLEASE / EOSINOPHIL / NUCLEASE / RIBONUCLEASE / RNASE US / RNASE-2 / INHIBITOR / 5'-ATP / AP3A / AP4A / AP5A / CHEMOTAXIS / GLYCOPROTEIN / POLYMORPHISM / SENSORY TRANSDUCTION | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Baker, M.D. / Holloway, D.E. / Swaminathan, G.J. / Acharya, K.R. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Crystal Structures of Eosinophil-Derived Neurotoxin (Edn) in Complex with the Inhibitors 5'- ATP, Ap(3)A, Ap(4)A, and Ap(5)A. Authors: Baker, M.D. / Holloway, D.E. / Swaminathan, G.J. / Acharya, K.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c01.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c01.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 2c01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c01_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 2c01_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 2c01_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2c01_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/2c01 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/2c01 | HTTPS FTP |
-Related structure data
Related structure data | 2bzzC 2c02C 2c05C 1gqvS 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
#1: Protein | Mass: 15611.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: EOSINOPHIL / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P10153, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-ACY / |
#3: Chemical | ChemComp-ATP / |
#4: 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: 1.63 Å3/Da / Density % sol: 24.07 % |
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Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 203 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→40 Å / Num. obs: 36418 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 10.07 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 1.24→1.28 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 13.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GQV Resolution: 1.24→40 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: GAMMA PHOSPHATE OF ATP NOT MODELLED DUE TO POOR DENSITY. ALPHA AND BETA PHOSPHATES MODELLED IN TWO ALTERNATE CONFROMATIONS.
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Refinement step | Cycle: LAST / Resolution: 1.24→40 Å
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Refine LS restraints |
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