+Open data
-Basic information
Entry | Database: PDB / ID: 1dyt | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of ECP (RNase 3) at 1.75 A | ||||||
Components | EOSINOPHIL CATIONIC PROTEIN | ||||||
Keywords | HYDROLASE / EOSINOPHIL CATIONIC PROTEIN / ECP / RNASE 3 | ||||||
Function / homology | Function and homology information induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide ...induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / endonuclease activity / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / innate immune response / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Mallorqui-Fernandez, G. / Pous, J. / Peracaula, R. / Maeda, T. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Rueth, F.X. / Coll, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Three-Dimensional Crystal Structure of Human Eosinophil Cationic Protein (Rnase 3) at 1.75 A Resolution. Authors: Mallorqui-Fernandez, G. / Pous, J. / Peracaula, R. / Maeda, T. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Rueth, F.X. / Coll, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dyt.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dyt.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dyt ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dyt | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15598.876 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: EOSINOPHIL / Gene: RNASE3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | #3: Chemical | ChemComp-CIT / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.2 Details: 8% JEFFAMINE M-600, 0.1M SODIUM CITRATE PH 5.2, 0.01M IRON CHLORIDE | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.05271 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: TOROIDAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05271 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→22 Å / Num. obs: 35401 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 1.75 / Rsym value: 0.03 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 58607 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.03 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EOSINOPHIL DERIVED PROTEIN Resolution: 1.75→20 Å / Rfactor Rfree error: 8.0E-5 / Data cutoff high absF: 10000 / Cross valid method: MLF / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: DENSITY MODIFICATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.403 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9A / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |