[English] 日本語
Yorodumi- PDB-3txj: HEWL co-crystallization with NAG with silicone oil as the cryopro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3txj | ||||||
---|---|---|---|---|---|---|---|
Title | HEWL co-crystallization with NAG with silicone oil as the cryoprotectant | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / hen egg white lysozyme (HEWL) / bacterial cell wall lysis | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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: 2.48 Å | ||||||
Authors | Tanley, S.W.M. / Schreurs, A.M.M. / Helliwell, J.R. / Kroon-Batenburg, L.M.J. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2013 Title: Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals. Authors: Tanley, S.W. / Schreurs, A.M. / Helliwell, J.R. / Kroon-Batenburg, L.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3txj.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3txj.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 3txj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/3txj ftp://data.pdbj.org/pub/pdb/validation_reports/tx/3txj | HTTPS FTP |
---|
-Related structure data
Related structure data | 3txbC 3txdC 3txeC 3txfC 3txgC 3txhC 3txiC 3txkC 2w1yS 3txc 3txl C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Sugar | ChemComp-NAG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.72 % |
---|---|
Crystal grow | Temperature: 295 K / Method: batch / pH: 4.7 Details: 49 mg HEWL + 117 mg N-acetylglucosamine in 1 mL 0.04 M sodium acetate + 1 mL 10% sodium chloride, with silicone oil as cryoprotectant, pH 4.7, BATCH, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2011 / Details: Osmic Confocal Max-Flux, blue configuration |
Radiation | Monochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→55.53 Å / Num. all: 4343 / Num. obs: 4126 / % possible obs: 95 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 12.99 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.199 / Rsym value: 0.199 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.48→2.57 Å / Redundancy: 11.55 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 4.8 / Num. unique all: 4343 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W1Y Resolution: 2.48→55.53 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.848 / SU B: 13.614 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 32.315 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→55.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.48→2.547 Å / Total num. of bins used: 20
|