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Yorodumi- PDB-4a2o: STRUCTURE OF THE HUMAN EOSINOPHIL CATIONIC PROTEIN IN COMPLEX WIT... -
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-Basic information
Entry | Database: PDB / ID: 4a2o | ||||||
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Title | STRUCTURE OF THE HUMAN EOSINOPHIL CATIONIC PROTEIN IN COMPLEX WITH SULFATE ANIONS | ||||||
Components | EOSINOPHIL CATIONIC PROTEIN | ||||||
Keywords | HYDROLASE / OXIDOREDUCTASE / ANTIMICROBIAL / CYTOTOXIC | ||||||
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 / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Boix, E. / Pulido, D. / Moussaoui, M. / Nogues, V. / Russi, S. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 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, V. / Russi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a2o.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a2o.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a2o_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 4a2o_full_validation.pdf.gz | 456 KB | Display | |
Data in XML | 4a2o_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4a2o_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/4a2o ftp://data.pdbj.org/pub/pdb/validation_reports/a2/4a2o | HTTPS FTP |
-Related structure data
Related structure data | 4a2yC 1dytS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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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.) HOMO SAPIENS (human) / Cell: EOSINOPHIL / Plasmid: PET11C/ECP / 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-SO4 / #3: Water | ChemComp-HOH / | Sequence details | RECOMBINANT PROTEIN EXPRESSED USING A SYNTHETIC GENE (BOIX ET AL. J.BIOL.CHEM. 274, 15605) BASED ON ...RECOMBINAN | |
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-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: 24.17 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→51.62 Å / Num. obs: 25341 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 90.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DYT Resolution: 1.69→51.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.42 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-27 OF P12724 ARE THE SIGNAL PEPTIDE. LOOP 90-92 IS PARTIALLY DISORDERED SIDE CHAINS OF R28, W35, R73, F76, R101, AND R105 ARE PARTIALLY DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.866 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→51.62 Å
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