[English] 日本語
Yorodumi- PDB-3b6l: Crystal structure of lysozyme folded in SDS and 2-methyl-2,4-pent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b6l | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of lysozyme folded in SDS and 2-methyl-2,4-pentanediol | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / egg-white lysozyme / protein-SDS complex / MPD / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase | ||||||
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 / AB INITIO / Resolution: 2.3 Å | ||||||
Authors | Michaux, C. / Pouyez, J. / Wouters, J. / Prive, G.G. | ||||||
Citation | Journal: BMC Struct.Biol. / Year: 2008 Title: Protecting role of cosolvents in protein denaturation by SDS: a structural study. Authors: Michaux, C. / Pouyez, J. / Wouters, J. / Prive, G.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3b6l.cif.gz | 41.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3b6l.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 3b6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/3b6l ftp://data.pdbj.org/pub/pdb/validation_reports/b6/3b6l | HTTPS FTP |
---|
-Related structure data
Related structure data | 3b72C 1z55S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme |
---|---|
#2: Chemical | ChemComp-SDS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100mM sodium acetate buffer pH 4.6 and 2M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: BRUKER PROTEUM / Detector: CCD / Date: Nov 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→34.7 Å / Num. obs: 5468 / % possible obs: 99.7 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.9 |
Reflection shell | Highest resolution: 2.3 Å / Rmerge(I) obs: 0.022 / Mean I/σ(I) obs: 8.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO Starting model: 1Z55 Resolution: 2.3→34.7 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.903 / Num. parameters: 4351 / Num. restraintsaints: 4208 / SU B: 4.978 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.621 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 16.934 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1083 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→34.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
|