[English] 日本語
Yorodumi- PDB-6qq3: The room temperature structure of lysozyme via the acoustic levit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qq3 | ||||||
---|---|---|---|---|---|---|---|
Title | The room temperature structure of lysozyme via the acoustic levitation of a droplet | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme HEWL hydrolase / acoustic levitation | ||||||
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 / Resolution: 1.53 Å | ||||||
Authors | Axford, D.N. / Docker, P. / Dye, E. / Morris, R. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Non-Contact Universal Sample Presentation for Room Temperature Macromolecular Crystallography Using Acoustic Levitation. Authors: Morris, R.H. / Dye, E.R. / Axford, D. / Newton, M.I. / Beale, J.H. / Docker, P.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qq3.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qq3.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/6qq3 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qq3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5kxoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00698, lysozyme | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.02 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 10 % w/v NaCl, 25 % w/v ethylene glycol, 100 mM Na Acetate pH 4.8 |
-Data collection
Diffraction | Mean temperature: 294 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2018 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→39.74 Å / Num. obs: 18767 / % possible obs: 99.5 % / Redundancy: 101.5 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.984 / R split: 0.101 / Net I/σ(I): 3.52 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 0.71 / Num. unique obs: 884 / CC1/2: 0.665 / R split: 0.549 / % possible all: 95 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5kxo Resolution: 1.53→39.724 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.18
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→39.724 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|