+Open data
-Basic information
Entry | Database: PDB / ID: 2b5z | ||||||
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Title | Hen lysozyme chemically glycosylated | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / chemical glycosylation | ||||||
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 / Resolution: 1.6 Å | ||||||
Authors | Lopez-Jaramillo, F.J. / Perez-Balderas, F. / Hernandez-Mateo, F. / Santoyo-Gonzalez, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Production, crystallization and X-ray characterization of chemically glycosylated hen egg-white lysozyme. Authors: Lopez-Jaramillo, F.J. / Perez-Banderas, F. / Hernandez-Mateo, F. / Santoyo-Gonzalez, F. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Production, crystallization and X-ray characterization of chemically glycosylated hen egg-white lysozyme Authors: Lopez-Jaramillo, F.J. / Perez-Balderas, F. / Hernandez-Mateo, F. / Santoyo-Gonzalez, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b5z.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b5z.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 2b5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/2b5z ftp://data.pdbj.org/pub/pdb/validation_reports/b5/2b5z | HTTPS FTP |
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-Related structure data
Related structure data | 1ieeS 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 / Source method: isolated from a natural source / Details: hen egg / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Sugar | ChemComp-BGS / ( #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.03 Å3/Da / Density % sol: 38.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: Magnesium Sulfate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 22, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→19.57 Å / Num. obs: 19330 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.17 % / Biso Wilson estimate: 19.2 Å2 / Limit h max: 19 / Limit h min: 0 / Limit k max: 21 / Limit k min: 0 / Limit l max: 79 / Limit l min: 0 / Observed criterion F max: 939492.49 / Observed criterion F min: 3.804 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 22.19 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 5.08 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6.78 / Num. unique all: 2774 / Rsym value: 0.25 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IEE Resolution: 1.6→9.88 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.98 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 65.3983 Å2 / ksol: 0.546683 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.73 Å2 / Biso mean: 20.58 Å2 / Biso min: 9.38 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→9.88 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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