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Yorodumi- PDB-4b0d: CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME FROM AN AUTO HARVESTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b0d | ||||||
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Title | CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME FROM AN AUTO HARVESTED CRYSTAL | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / AUTOMATION / HIGH-THROUGHPUT CRYSTALLIZATION / CRYSTAL MOUNTING / CRYSTALLIZATION MICROPLATES | ||||||
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: 1.1 Å | ||||||
Authors | Cipriani, F. / Rower, M. / Landret, C. / Zander, U. / Felisaz, F. / Marquez, J.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Crystal Direct: A New Method for Automated Crystal Harvesting Based on Laser-Induced Photoablation of Thin Films Authors: Cipriani, F. / Rower, M. / Landret, C. / Zander, U. / Felisaz, F. / Marquez, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b0d.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b0d.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 4b0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/4b0d ftp://data.pdbj.org/pub/pdb/validation_reports/b0/4b0d | 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: P00698, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.26 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→39 Å / Num. obs: 48335 / % possible obs: 100 % / Observed criterion σ(I): 2.9 / Redundancy: 13.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.81 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→34.12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.123 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.206 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→34.12 Å
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