+Open data
-Basic information
Entry | Database: PDB / ID: 4cj2 | ||||||
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Title | Crystal structure of HEWL in complex with affitin H4 | ||||||
Components |
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Keywords | HYDROLASE/DE NOVO PROTEIN / HYDROLASE-DE NOVO PROTEIN COMPLEX / GLYCOSIDASE | ||||||
Function / homology | Function and homology information RNA endonuclease activity / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...RNA endonuclease activity / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / DNA binding / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | SULFOLOBUS ACIDOCALDARIUS (acidophilic) GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Correa, A. / Pacheco, S. / Mechaly, A.E. / Obal, G. / Behar, G. / Mouratou, B. / Oppezzo, P. / Alzari, P.M. / Pecorari, F. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Potent and Specific Inhibition of Glycosidases by Small Artificial Binding Proteins (Affitins) Authors: Correa, A. / Pacheco, S. / Mechaly, A.E. / Obal, G. / Behar, G. / Mouratou, B. / Oppezzo, P. / Alzari, P.M. / Pecorari, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cj2.cif.gz | 180 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cj2.ent.gz | 142.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/4cj2 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/4cj2 | HTTPS FTP |
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-Related structure data
Related structure data | 4cj0C 4cj1C 1gwdS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 16257.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme #2: Protein | Mass: 9053.286 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13123*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46.45 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Type: ESRF / Wavelength: 0.97 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.05 Å / Num. obs: 62347 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GWD Resolution: 1.5→43.08 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.413 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.116 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→43.08 Å
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Refine LS restraints |
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