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Yorodumi- PDB-7o2o: Lysozyme structure from microfluidic-based in situ data collection -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o2o | ||||||
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Title | Lysozyme structure from microfluidic-based in situ data collection | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.833 Å | ||||||
Authors | Gardais, A. / Chavas, L. | ||||||
Citation | Journal: Micromachines (Basel) / Year: 2022 Title: Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments. Authors: Vasireddi, R. / Gardais, A. / Chavas, L.M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o2o.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o2o.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 7o2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/7o2o ftp://data.pdbj.org/pub/pdb/validation_reports/o2/7o2o | HTTPS FTP |
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-Related structure data
Related structure data | 1lyzS 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: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | #3: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Temperature: 283.15 K / Method: microfluidic Details: 50 mM NaOAc/HOAc, pH 3.5 1 M NaCl 35% EG, 12.5% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 298.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.833→56.28 Å / Num. obs: 11146 / % possible obs: 100 % / Redundancy: 27.5 % / Biso Wilson estimate: 28.68 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.021 / Rrim(I) all: 0.113 / Net I/av σ(I): 22.2 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.833→1.86 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 525 / CC1/2: 0.884 / Rpim(I) all: 0.2 / Rrim(I) all: 0.614 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1lyz Resolution: 1.833→56.28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.133 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.146 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.114
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Displacement parameters | Biso mean: 29.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.833→56.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.833→1.86 Å
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