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Yorodumi- PDB-6qqe: Room temperature structure of Hen Egg White Lysozyme recorded aft... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qqe | ||||||
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Title | Room temperature structure of Hen Egg White Lysozyme recorded after an accumulated dose of 20 kGy | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Lysozyme / disulphide bonds / radiation damage | ||||||
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 / SYNCHROTRON / Resolution: 1.37 Å | ||||||
Authors | Gotthard, G. / Aumonier, S. / Royant, A. | ||||||
Citation | Journal: Iucrj / Year: 2019 Title: Specific radiation damage is a lesser concern at room temperature. Authors: Gotthard, G. / Aumonier, S. / De Sanctis, D. / Leonard, G. / von Stetten, D. / Royant, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qqe.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qqe.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qqe_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 6qqe_full_validation.pdf.gz | 421.9 KB | Display | |
Data in XML | 6qqe_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 6qqe_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/6qqe ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qqe | HTTPS FTP |
-Related structure data
Related structure data | 6qq8C 6qq9C 6qqaC 6qqbC 6qqcC 6qqdC 6qqfC 6qqhC 6qqiC 6qqjC 6qqkC 6qsaC 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 genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: 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: 2.08 Å3/Da / Density % sol: 40.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 6-9% NaCl, 0.1M Na Acetate pH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2016 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→39.62 Å / Num. obs: 25762 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 24.97 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.37→1.41 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1828 / CC1/2: 0.7 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Resolution: 1.37→39.61 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.291 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.929 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→39.61 Å
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Refine LS restraints |
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