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Yorodumi- PDB-2cgi: Siras structure of tetragonal lysozyme using derivative data coll... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cgi | ||||||
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Title | Siras structure of tetragonal lysozyme using derivative data collected at the high energy remote Holmium Kedge | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / HIGH ENERGY / PHASING / MAD / SAD / SIRAS / RADIATION DAMAGE / ABSORPTION / HOLMIUM / GLYCOSIDASE / ALLERGEN / ANTIMICROBIAL / BACTERIOLYTIC ENZYME | ||||||
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 / SIRAS / Resolution: 1.35 Å | ||||||
Authors | Jakoncic, J. / Di Michiel, M. / Zhong, Z. / Honkimaki, V. / Jouanneau, Y. / Stojanoff, V. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2006 Title: Anomalous Diffraction at Ultra-High Energy for Protein Crystallography. Authors: Jakoncic, J. / Di Michiel, M. / Zhong, Z. / Honkimaki, V. / Jouanneau, Y. / Stojanoff, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cgi.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cgi.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 2cgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/2cgi ftp://data.pdbj.org/pub/pdb/validation_reports/cg/2cgi | 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: Chemical | ChemComp-CL / |
#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: 1.9 Å3/Da / Density % sol: 37 % |
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Crystal grow | pH: 4.5 / Details: pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID15A / Wavelength: 0.219 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.219 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→25 Å / Num. obs: 26207 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 19.5 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 19 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.35→19.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.053 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.06 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→19.07 Å
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Refine LS restraints |
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