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Yorodumi- PDB-5amy: Crystal Structure of Hen egg white lysozyme processed with the Cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5amy | ||||||
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Title | Crystal Structure of Hen egg white lysozyme processed with the CrystalDirect automated mounting and cryo-cooling technology | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / AUTOMATED CRYSTAL HARVESTING / AUTOMATED CRYO-COOLING / CRYSTALDIRECT | ||||||
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 / OTHER / Resolution: 1.8 Å | ||||||
Authors | Zander, U. / Hoffmann, G. / Cornaciu, I. / Cipriani, F. / Marquez, J.A. | ||||||
Citation | Journal: To be Published Title: Automated Harvesting and Processing of Protein Crystals Through Laser Photoablation. Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5amy.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5amy.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 5amy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5amy ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amy | HTTPS FTP |
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-Related structure data
Related structure data | 5an2 |
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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: obtained synthetically / Source: (synth.) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.89 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM ACETATE, 1.25 M NACL, PH=4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91787 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91787 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 10961 / % possible obs: 99.5 % / Observed criterion σ(I): 2.5 / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 |
-Processing
Software | Name: REFMAC / Version: 5.8.0123 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.8→27.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.23 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY
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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: 22.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.51 Å
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Refine LS restraints |
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