+Open data
-Basic information
Entry | Database: PDB / ID: 5b59 | ||||||
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Title | Hen egg-white lysozyme modified with a keto-ABNO. | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Catalyst / Modification | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sasaki, D. / Seki, Y. / Sohma, Y. / Oisaki, K. / Kanai, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Transition Metal-Free Tryptophan-Selective Bioconjugation of Proteins Authors: Seki, Y. / Ishiyama, T. / Sasaki, D. / Abe, J. / Sohma, Y. / Oisaki, K. / Kanai, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b59.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b59.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b59 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b59 | HTTPS FTP |
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-Related structure data
Related structure data | 2lyzS S: Starting model for refinement |
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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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Details: W62 is modified with leto-ABNO. / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#2: Chemical | ChemComp-KTO / ( |
#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: 2.01 Å3/Da / Density % sol: 38.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.8M NaCl, 0.05M AcOH |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 8266 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rsym value: 0.053 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4 % / Mean I/σ(I) obs: 9.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LYZ Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.841 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.938 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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