+Open data
-Basic information
Entry | Database: PDB / ID: 3a34 | ||||||
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Title | Effect of Ariginine on lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / glycosidase / arginine / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ito, L. / Shiraki, K. / Matsuura, T. / Yamaguchi, H. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Implication of Arg bindings on aromatic surfaces of lysozyme for additives that prevent protein aggregation Authors: Ito, L. / Shiraki, K. / Matsuura, T. / Yamaguchi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a34.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a34.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 3a34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/3a34 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/3a34 | HTTPS FTP |
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-Related structure data
Related structure data | 1helS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: EGG / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 124 molecules
#2: Chemical | ChemComp-ARG / #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-ACT / | #6: 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 Å3/Da / Density % sol: 38.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 15, 2008 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→33.69 Å / Num. obs: 13045 / Redundancy: 6.4 % / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 6.5 / % possible all: 48.7 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HEL Resolution: 1.65→33.69 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.831 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.122 / 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: 12.941 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→33.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Total num. of bins used: 20
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