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- PDB-4x08: Structure of H128N/ECP mutant in complex with sulphate anions at ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x08 | ||||||
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Title | Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms. | ||||||
![]() | Eosinophil cationic protein | ||||||
![]() | HYDROLASE / active centre mutation / sulphate / sulphate recognition site / ECP | ||||||
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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blanco, J.A. / Garcia, J.M. / Salazar, V.A. / Sanchez, D. / Moussauoi, M. / Boix, E. | ||||||
![]() | ![]() Title: Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms. Authors: Blanco, J.A. / Garcia, J.M. / Salazar, V.A. / Sanchez, D. / Moussauoi, M. / Boix, E. #1: ![]() Title: The sulfate-binding site structure of the human eosinophil cationic protein as revealed by a new crystal form. Authors: Boix, E. / Pulido, D. / Moussaoui, M. / Nogues, M.V. / Russi, S. #2: ![]() 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. / Aymami, J. / Maeda, T. / Tada, H. / Yamada, H. / Seno, M. / de Llorens, R. / Gomis-Ruth, 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 | ![]() | 84 KB | Display | ![]() |
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PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4a2oS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15706.027 Da / Num. of mol.: 2 / Mutation: H128N Source method: isolated from a genetically manipulated source Details: Residue 97 corresponds to a protein natural variant Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters, EC: 3.1.27.5 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.01 % / Description: NEEDLE-SHAPED CRYSTALS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: CRYSTALS GREW FROM A CRYSTALLISATION CONDITION BASED ON 0.2M LITHIUM SULPHATE, 0.1M TRIS BUFFER, pH8.5 AND 15% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→41.37 Å / Num. all: 54033 / Num. obs: 54033 / % possible obs: 98.8 % / Redundancy: 1.82 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.34→1.39 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4A2O Resolution: 1.34→41.37 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→41.37 Å
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Refine LS restraints |
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LS refinement shell |
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