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Yorodumi- PDB-6qqd: Cryogenic temperature structure of Hen Egg White Lysozyme recorde... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qqd | ||||||
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Title | Cryogenic temperature structure of Hen Egg White Lysozyme recorded after an accumulated dose of 10 MGy | ||||||
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: 1.92 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 | 6qqd.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qqd.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 6qqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qqd_validation.pdf.gz | 424 KB | Display | wwPDB validaton report |
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Full document | 6qqd_full_validation.pdf.gz | 425.5 KB | Display | |
Data in XML | 6qqd_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 6qqd_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/6qqd ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qqd | HTTPS FTP |
-Related structure data
Related structure data | 6qq8C 6qq9C 6qqaC 6qqbC 6qqcC 6qqeC 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 | ChemComp-CL / #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: 1.98 Å3/Da / Density % sol: 37.93 % |
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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: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 28, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→33.71 Å / Num. obs: 8490 / % possible obs: 91.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.699 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.34 |
Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.88 / Num. unique obs: 640 / CC1/2: 0.706 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Resolution: 1.92→33.71 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.628 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.169 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.932 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→33.71 Å
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Refine LS restraints |
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