+Open data
-Basic information
Entry | Database: PDB / ID: 1yl0 | ||||||
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Title | Effect of alcohols on protein hydration | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Hen egg white lysozyme / alcohols / hydration / water structure | ||||||
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: 1.9 Å | ||||||
Authors | Deshpande, A. / Nimsadkar, S. / Mande, S.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Effect of alcohols on protein hydration: crystallographic analysis of hen egg-white lysozyme in the presence of alcohols. Authors: Deshpande, A. / Nimsadkar, S. / Mande, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yl0.cif.gz | 39.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yl0.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/1yl0 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/1yl0 | HTTPS FTP |
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-Related structure data
Related structure data | 1ykxC 1ykyC 1ykzC 1yl1C 1z55C 2lymS 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
#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: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | #5: 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: 2.13 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium chloride, sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→22.54 Å / Num. all: 11677 / Num. obs: 6364 / Redundancy: 0.98 % / Biso Wilson estimate: 22.22 Å2 / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 0.98 % / Rmerge(I) obs: 0.069 / Num. unique all: 11644 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LYM Resolution: 1.9→22.54 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→22.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.01 Å / Rfactor Rfree error: 0.01
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