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Yorodumi- PDB-8a9r: Tetragonal Hen Egg-White (HEW) Lysozyme soaked in reduced resazur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a9r | ||||||
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Title | Tetragonal Hen Egg-White (HEW) Lysozyme soaked in reduced resazurin in a glovebox and flash-cooled using a miniature-airlock | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / anaerobic crystallisation / glove box / methodology | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | van der Linden, P. / Engilberge, S. / Atta, M. / Carpentier, P. | ||||||
Funding support | 1items
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Citation | Journal: J.Appl.Crystallogr. / Year: 2022 Title: A miniature airlock system to aid the cryo-cooling of protein crystals grown under anoxic conditions Authors: Engilberge, S. / Atta, M. / Carpentier, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a9r.cif.gz | 43 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a9r.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 8a9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a9r_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 8a9r_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 8a9r_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 8a9r_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/8a9r ftp://data.pdbj.org/pub/pdb/validation_reports/a9/8a9r | HTTPS FTP |
-Related structure data
Related structure data | 2xbrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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) / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM sodium acetate pH 4.6, 1M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 15200 / % possible obs: 98.8 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rrim(I) all: 0.093 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.59→1.7 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2299 / CC1/2: 0.597 / Rrim(I) all: 1.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XBR Resolution: 1.6→33 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 74.91 Å2 / Biso mean: 28.8354 Å2 / Biso min: 17.13 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→33 Å
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