+Open data
-Basic information
Entry | Database: PDB / ID: 6pbb | |||||||||
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Title | Crystal structure of Hen Egg White Lysozyme in complex with I3C | |||||||||
Components | Lysozyme | |||||||||
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 / SAD / Resolution: 1.89151078799 Å | |||||||||
Authors | Truong, J.Q. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68. Authors: Truong, J.Q. / Panjikar, S. / Shearwin-Whyatt, L. / Bruning, J.B. / Shearwin, K.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pbb.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pbb.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 6pbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/6pbb ftp://data.pdbj.org/pub/pdb/validation_reports/pb/6pbb | HTTPS FTP |
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-Related 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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: B8YK79, UniProt: P00698*PLUS, lysozyme | ||||||
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#2: Chemical | ChemComp-I3C / #3: Chemical | ChemComp-CL / | #4: 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: 1.98 Å3/Da / Density % sol: 38 % / Description: Rectangular prism |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.459 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→38.2 Å / Num. obs: 9810 / % possible obs: 98.4 % / Redundancy: 43.7 % / Biso Wilson estimate: 26.8218497582 Å2 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.87→1.92 Å / Num. unique obs: 475 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.89151078799→34.5070010288 Å / SU ML: 0.243569862865 / Cross valid method: FREE R-VALUE / σ(F): 1.90937325444 / Phase error: 27.2332016465
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.3201983581 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89151078799→34.5070010288 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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