+Open data
-Basic information
Entry | Database: PDB / ID: 4ias | ||||||
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Title | HEW Lysozyme by langmuir- blodgett modified vapour diffusion | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Langmuir-Blodgett / Thin-film | ||||||
Function / homology | Function and homology information 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 ...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 / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Belmonte, L. / Pechkova, E. / Riekel, C. / Scudieri, D. / Nicolini, C. | ||||||
Citation | Journal: To be Published Title: Laser - microdissection of protein crystals down to submicron dimensions Authors: Pechkova, E. / Belmonte, L. / Riekel, C. / Popov, D. / Koenig, C. / Nicolini, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ias.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ias.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ias.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/4ias ftp://data.pdbj.org/pub/pdb/validation_reports/ia/4ias | HTTPS FTP |
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-Related 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: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.53 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→55.671 Å / Num. all: 3906 / Num. obs: 3906 / % possible obs: 100 % / Redundancy: 12.3 % / Rsym value: 0.242 / Net I/σ(I): 20.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→55.67 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.798 / WRfactor Rfree: 0.3295 / WRfactor Rwork: 0.2173 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7859 / SU B: 14.116 / SU ML: 0.302 / SU Rfree: 0.4251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 39.54 Å2 / Biso mean: 9.4788 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→55.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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