+Open data
-Basic information
Entry | Database: PDB / ID: 6qx0 | ||||||
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Title | HEWL lysozyme, crystallized from LiCl solution | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
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: 1.35 Å | ||||||
Authors | Boikova, A.S. / Dorovatovskii, P.V. / Dyakova, Y.A. / Ilina, K.B. / Kuranova, I.P. / Lazarenko, V.A. / Marchenkova, M.A. / Pisarevsky, Y.V. / Timofeev, V.I. / Kovalchuk, M.V. | ||||||
Citation | Journal: To Be Published Title: HEWL lysozyme, crystallized from different chlorides Authors: Boikova, A.S. / Dorovatovskii, P.V. / Dyakova, Y.A. / Ilina, K.B. / Kuranova, I.P. / Lazarenko, V.A. / Marchenkova, M.A. / Pisarevsky, Y.V. / Timofeev, V.I. / Kovalchuk, M.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qx0.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qx0.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/6qx0 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/6qx0 | HTTPS FTP |
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-Related structure data
Related structure data | 6qwwC 6qwxC 6qwyC 6qwzC 4wldS S: Starting model for refinement C: citing same article (ref.) |
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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
#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 | #3: 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: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.80241 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.80241 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→27.85 Å / Num. obs: 26221 / % possible obs: 92.66 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.35→1.385 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WLD Resolution: 1.35→27.85 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.353 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.066 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.753 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→27.85 Å
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Refine LS restraints |
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