[English] 日本語
Yorodumi- PDB-3zek: Hen egg-white lysozyme structure determined at room temperature b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zek | ||||||
---|---|---|---|---|---|---|---|
Title | Hen egg-white lysozyme structure determined at room temperature by in- situ diffraction in ChipX | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / MICROFLUIDIC CHIP / IN-SITU DIFFRACTION | ||||||
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: 1.43 Å | ||||||
Authors | Pinker, F. / Lorber, B. / Sauter, C. | ||||||
Citation | Journal: To be Published Title: Chipx: A Novel Microfluidic Chip for Counter- Diffusion Crystallization of Biomolecules and in Situ Crystal Analysis at Room Temperature Authors: Pinker, F. / Brun, M. / Morin, P. / Deman, A. / Chateaux, J. / Olieric, V. / Stirnimann, C. / Lorber, B. / Terrier, N. / Ferrigno, R. / Sauter, C. #1: Journal: Lab Chip / Year: 2009 Title: Microfluidic Chips for the Crystallization of Biomacromolecules by Counter-Diffusion and on-Chip Crystal X-Ray Analysis. Authors: Dhouib, K. / Khan Malek, C. / Pfleging, W. / Gauthier-Manuel, B. / Duffait, R. / Thuillier, G. / Ferrigno, R. / Jacquamet, L. / Ohana, J. / Ferrer, J. / Theobald-Dietrich, A. / Giege, R. / ...Authors: Dhouib, K. / Khan Malek, C. / Pfleging, W. / Gauthier-Manuel, B. / Duffait, R. / Thuillier, G. / Ferrigno, R. / Jacquamet, L. / Ohana, J. / Ferrer, J. / Theobald-Dietrich, A. / Giege, R. / Lorber, B. / Sauter, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zek.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zek.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/3zek ftp://data.pdbj.org/pub/pdb/validation_reports/ze/3zek | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zejC 1ieeS C: citing same article (ref.) 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 natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 4.5 Details: LYSOZYME WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 50 MG/ML LYSOZYME SOLUTION CONTAINING 0.3% BETA-OCTYL- ...Details: LYSOZYME WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 50 MG/ML LYSOZYME SOLUTION CONTAINING 0.3% BETA-OCTYL-GLUCOSIDE (M/V) TO FACILITATE SAMPLE LOADING BY CAPILLARITY. CRYSTALLANT RESERVOIRS WERE FILLED WITH 1 M NACL CONTAINING 30% (M/V) PEG-3350 OR 2 M NACL, AND 0.1 M SODIUM ACETATE PH 4.5. |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→30 Å / Num. obs: 22727 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.43→1.52 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.7 / % possible all: 97.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IEE Resolution: 1.43→27.415 Å / SU ML: 0.13 / σ(F): 3.28 / Phase error: 18.2 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→27.415 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|