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Yorodumi- PDB-1uc0: Crystal structure of wild-type hen-egg white lysozyme singly labe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uc0 | |||||||||
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Title | Crystal structure of wild-type hen-egg white lysozyme singly labeled with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / Protein-carbohydrate 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 / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...Lactose synthesis / 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: 1.85 Å | |||||||||
Authors | Muraki, M. / Harata, K. | |||||||||
Citation | Journal: J.MOL.RECOG. / Year: 2003 Title: X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine Authors: Muraki, M. / Harata, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uc0.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uc0.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 1uc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/1uc0 ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1uc0 | 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
#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 | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-GOL / |
#4: 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: 1.88 Å3/Da / Density % sol: 34.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: sodium acetate, sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
Crystal grow | *PLUS Method: vapor diffusion / Details: used microseeding |
Components of the solutions | *PLUS Conc.: 50 mM / Common name: sodium acetate / Details: pH4.5 |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: ENRAF-NONIUS FAST / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→27.6 Å / Num. obs: 74009 / % possible obs: 90.8 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.258 |
Reflection | *PLUS Num. obs: 10897 / Redundancy: 6.8 % / Num. measured all: 74099 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Wild-type Hen-egg white lysozyme Resolution: 1.85→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 14.89 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.19 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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