+Open data
-Basic information
Entry | Database: PDB / ID: 4owz | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of ECP/H15A mutant. | ||||||
Components | Eosinophil cationic protein | ||||||
Keywords | HYDROLASE / RNase 3 / Eosinophil Cationic Protein | ||||||
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 / Resolution: 1.47 Å | ||||||
Authors | Blanco, J.A. / Salazar, V.A. / Boix, E. / Moussaoui, M. | ||||||
Funding support | Spain, 1items
| ||||||
Citation | Journal: To be published Title: Structure of a ECP/H15A mutant at 1.47 Angstroms resolution Authors: Blanco, J.A. / Salazar, V.A. / Boix, E. / Moussaoui, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4owz.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4owz.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 4owz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/4owz ftp://data.pdbj.org/pub/pdb/validation_reports/ow/4owz | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 15663.004 Da / Num. of mol.: 2 / Mutation: H15A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Bone marrow / Cell: Eosinophil / Gene: ECP,RNASE3,RNS3 / Plasmid: pET11c / 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 | ChemComp-CIT / #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | AUTHORS STATE THAT BOTH IRON AND CITRATE ATOMS HAVE BEEN ADJUSTED TO THE CORRESPONDING ELECTRON ...AUTHORS STATE THAT BOTH IRON AND CITRATE ATOMS HAVE BEEN ADJUSTED TO THE CORRESPOND | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: Protein was resuspended in 20mM sodium acetate buffer, pH 5.0, 1 uL of sample mixed with 1 uL of crystallisation buffer (0.1M sodium citrate, pH 5.2; 8% Jeffamine M-600; 10mM iron(III) chloride) PH range: 5.0-5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→175.23 Å / Num. obs: 60201 / % possible obs: 100 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 1.47→1.58 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 6.8 / % possible all: 100 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.47→25.452 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→25.452 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|