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Yorodumi- PDB-7ol8: Crystal structure of Lysozyme in complex with trifluoroethanol: o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ol8 | ||||||
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Title | Crystal structure of Lysozyme in complex with trifluoroethanol: orthorhombic form | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / TFE complex | ||||||
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 / molecular replacement / Resolution: 1.15 Å | ||||||
Authors | Camara-Artigas, A. / Salinas-Garcia, M.C. / Plaza-Garrido, M. | ||||||
Funding support | Spain, 1items
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Citation | Journal: To be published Title: Crystal structure of Lysozyme in complex with TFE Authors: Camara-Artigas, A. / Salinas-Garcia, M.C. / Plaza-Garrido, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ol8.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ol8.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ol8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/7ol8 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/7ol8 | HTTPS FTP |
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-Related structure data
Related structure data | 7ol7C 6f1oS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 14331.160 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 | ChemComp-SO4 / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.3M NaCl, 0.1M MES, 10mM NaH2PO4 plus 20% TFE in the reservoir |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976256 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976256 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→19.34 Å / Num. obs: 39025 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.023 / Rrim(I) all: 0.056 / Net I/σ(I): 14.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F1O Resolution: 1.15→19.34 Å / SU ML: 0.0979 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 18.4765 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→19.34 Å
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Refine LS restraints |
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LS refinement shell |
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