+Open data
-Basic information
Entry | Database: PDB / ID: 4eta | ||||||
---|---|---|---|---|---|---|---|
Title | Lysozyme, room temperature, 400 kGy dose | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.91 Å | ||||||
Authors | Boutet, S. / Lomb, L. / Williams, G. / Barends, T. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D. / Steinbrener, J. / Shoeman, R. ...Boutet, S. / Lomb, L. / Williams, G. / Barends, T. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D. / Steinbrener, J. / Shoeman, R. / Messerschmidt, M. / Barty, A. / White, T. / Kassemeyer, S. / Kirian, R. / Seibert, M. / Montanez, P. / Kenney, C. / Herbst, R. / Hart, P. / Pines, J. / Haller, G. / Gruner, S. / Philllip, H. / Tate, M. / Hromalik, M. / Koerner, L. / van Bakel, N. / Morse, J. / Ghonsalves, W. / Arnlund, D. / Bogan, M. / Calemann, C. / Fromme, R. / Hampton, C. / Hunter, M. / Johansson, L. / Katona, G. / Kupitz, C. / Liang, M. / Martin, A. / Nass, K. / Redecke, L. / Stellato, F. / Timneanu, N. / Wang, D. / Zatsepin, N. / Schafer, D. / Defever, K. / Neutze, R. / Fromme, P. / Spence, J. / Chapman, H. / Schlichting, I. | ||||||
Citation | Journal: Science / Year: 2012 Title: High-resolution protein structure determination by serial femtosecond crystallography. Authors: Boutet, S. / Lomb, L. / Williams, G.J. / Barends, T.R. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D.P. / Steinbrener, J. / Shoeman, R.L. / Messerschmidt, M. / Barty, A. / White, T. ...Authors: Boutet, S. / Lomb, L. / Williams, G.J. / Barends, T.R. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D.P. / Steinbrener, J. / Shoeman, R.L. / Messerschmidt, M. / Barty, A. / White, T.A. / Kassemeyer, S. / Kirian, R.A. / Seibert, M.M. / Montanez, P.A. / Kenney, C. / Herbst, R. / Hart, P. / Pines, J. / Haller, G. / Gruner, S.M. / Philipp, H.T. / Tate, M.W. / Hromalik, M. / Koerner, L.J. / van Bakel, N. / Morse, J. / Ghonsalves, W. / Arnlund, D. / Bogan, M.J. / Caleman, C. / Fromme, R. / Hampton, C.Y. / Hunter, M.S. / Johansson, L.C. / Katona, G. / Kupitz, C. / Liang, M. / Martin, A.V. / Nass, K. / Redecke, L. / Stellato, F. / Timneanu, N. / Wang, D. / Zatsepin, N.A. / Schafer, D. / Defever, J. / Neutze, R. / Fromme, P. / Spence, J.C. / Chapman, H.N. / Schlichting, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4eta.cif.gz | 35.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4eta.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 4eta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/4eta ftp://data.pdbj.org/pub/pdb/validation_reports/et/4eta | HTTPS FTP |
---|
-Related structure data
Related structure data | 4et8C 4et9C 4etbC 4etcC 4etdC 4eteC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ChemComp-CL / |
#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: 41.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: grown in Linbro plates in hanging or sitting drop geometry. Drops of equal volume of protein (20 mg/ml) and reservoir solution (1 M NaAc pH 3.0, 9-10 % NaCl, 6 % PEG 6000) were mixed. For ...Details: grown in Linbro plates in hanging or sitting drop geometry. Drops of equal volume of protein (20 mg/ml) and reservoir solution (1 M NaAc pH 3.0, 9-10 % NaCl, 6 % PEG 6000) were mixed. For the measurements, the crystals were equilibrated in 1 M NaAc pH 3.4, 10 % NaCl, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2011 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.6 Å / Num. all: 10022 / Num. obs: 10022 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 99.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.91→35.464 Å / SU ML: 0.22 / σ(F): 2.05 / Phase error: 14.72 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.213 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→35.464 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|