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Open data
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Basic information
Entry | Database: PDB / ID: 1dyt | |||||||||
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Title | X-ray crystal structure of ECP (RNase 3) at 1.75 A | |||||||||
![]() | EOSINOPHIL CATIONIC PROTEIN | |||||||||
![]() | HYDROLASE / EOSINOPHIL CATIONIC PROTEIN / ECP / RNASE 3 | |||||||||
Function / homology | ![]() 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / azurophil granule lumen ...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 / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / azurophil granule lumen / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mallorqui-Fernandez, G. / Pous, J. / Peracaula, R. / Maeda, T. / Tada, H. / Yamada, H. / Seno, M. / De Llorens, R. / Gomis-Rueth, F.X. / Coll, M. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 58.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 398.7 KB | Display | ![]() |
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Full document | ![]() | 414.3 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15598.876 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | #3: Chemical | ChemComp-CIT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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Solvent computation | Solvent model: DENSITY MODIFICATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.403 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9A / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |