+Open data
-Basic information
Entry | Database: PDB / ID: 7br5 | ||||||
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Title | Lysozyme-sugar complex in H2O | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Sugar complex | ||||||
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 Å | ||||||
Authors | Tanaka, I. / Chatake, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Recent structural insights into the mechanism of lysozyme hydrolysis. Authors: Tanaka, I. / Nishinomiya, R. / Goto, R. / Shimazaki, S. / Chatake, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7br5.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7br5.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 7br5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7br5_validation.pdf.gz | 750.5 KB | Display | wwPDB validaton report |
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Full document | 7br5_full_validation.pdf.gz | 750.8 KB | Display | |
Data in XML | 7br5_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7br5_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/7br5 ftp://data.pdbj.org/pub/pdb/validation_reports/br/7br5 | HTTPS FTP |
-Related structure data
Related structure data | 7deqC 7derC 4wldS S: Starting model for refinement C: citing same article (ref.) |
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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 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: P00698, lysozyme | ||||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #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: 1.99 Å3/Da / Density % sol: 38.26 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 4.5 Details: 40mg/mL lysozyme containing 2.1mg/mL (GlcNAc)4, 0.7M NaCl in a buffer of 50mM sodium-acetate (pH4.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1→16.833 Å / Num. obs: 61904 / % possible obs: 98.47 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 72.2 |
Reflection shell | Resolution: 1→1.02 Å / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3096 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4wld Resolution: 1→16.833 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→16.833 Å
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Refine LS restraints |
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LS refinement shell |
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